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Zhou K, Zhang J, Yang L, Li G, Wu M. Genetic Diversity and Population Structure of Leptosphaeria biglobosa from the Winter Oilseed Rape Region in China. J Fungi (Basel) 2023; 9:1092. [PMID: 37998897 PMCID: PMC10672222 DOI: 10.3390/jof9111092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Phoma stem canker (blackleg), caused by the fungi Leptosphaeria maculans (anamorph Phoma lingam) and L. biglobosa, is one of the most devastating diseases in oilseed rape (Brassica napus L.) production worldwide. However, the population structure and genetic variation of L. biglobosa populations in China have rarely been investigated. Here, a collection of 214 fungal strains of blackleg from China (including Shaanxi, Jiangxi, Hubei, Jiangsu, Chongqing, Sichuan, Guangxi, Guizhou, Hunan, and Henan) and Europe (France and Ukraine) was identified as L. biglobosa. Three simple sequence repeat (SSR) markers were developed to characterize their population structure. The results showed that the Nei's average gene diversity ranged from 0.6771 for the population from Jiangsu to 0.3009 for the population from Hunan. In addition, most of the genetic variability (96%) occurred within groups and there were only relatively small amounts among groups (4.0%) (FST = 0.043, p = 0.042 < 0.05). Pairwise population differentiation (FST) suggested that significant genetic differentiation was observed between different L. biglobosa populations. Bayesian and unweighted average method analysis revealed that these L. biglobosa strains were clustered into three branches, and three European strains were similar to those from eastern China. The pathogenicity assay showed that those in Group III were significantly more virulent than those in Group I (t = 2.69, p = 0.016). The study also showed that Group III was dominant in Chinese L. biglobosa populations, which provides new insights for the further study of population evolution and the management of this pathogen.
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Affiliation(s)
- Kang Zhou
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zhang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Yang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
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Frąc M, Kaczmarek J, Jędryczka M. Metabolic Capacity Differentiates Plenodomus lingam from P. biglobosus Subclade 'brassicae', the Causal Agents of Phoma Leaf Spotting and Stem Canker of Oilseed Rape ( Brassica napus) in Agricultural Ecosystems. Pathogens 2022; 11:pathogens11010050. [PMID: 35055998 PMCID: PMC8778923 DOI: 10.3390/pathogens11010050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
In contrast to the long-lasting taxonomic classification of Plenodomus lingam and P. biglobosus as one species, formerly termed Leptosphaeria maculans, both species form separate monophyletic groups, comprising sub-classes, differing considerably with epidemiology towards Brassicaceae plants. Considering the great differences between P. lingam and P. biglobosus, we hypothesized their metabolic capacities vary to a great extent. The experiment was done using the FF microplates (Biolog Inc., Hayward, CA, USA) containing 95 carbon sources and tetrazolium dye. The fungi P. lingam and P. biglobosus subclade 'brassicae' (3 isolates per group) were cultured on PDA medium for 6 weeks at 20 °C and then fungal spores were used as inoculum of microplates. The test was carried out in triplicate. We have demonstrated that substrate richness, calculated as the number of utilized substrates (measured at λ490 nm), and the number of substrates allowing effective growth of the isolates (λ750 nm), showed significant differences among tested species. The most efficient isolate of P. lingam utilized 36 carbon sources, whereas P. biglobosus utilized 60 substrates. Among them, 25-29 carbon sources for P. lingam and 34-48 substrates for P. biglobosus were efficiently used, allowing their growth. Cluster analysis based on Senath criteria divided P. biglobosus into two groups and P. lingam isolates formed one group (33% similarity). We deduce the similarities between the tested species help them coexist on the same host plant and the differences greatly contribute to their different lifestyles, with P. biglobosus being less specialized and P. lingam coevolving more strictly with the host plant.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland;
| | - Joanna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
- Correspondence:
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Czubatka-Bieńkowska A, Kaczmarek J, Marzec-Schmidt K, Nieróbca A, Czajka A, Jędryczka M. Country-Wide qPCR Based Assessment of Plasmodiophora brassicae Spread in Agricultural Soils and Recommendations for the Cultivation of Brassicaceae Crops in Poland. Pathogens 2020; 9:pathogens9121070. [PMID: 33419297 PMCID: PMC7766057 DOI: 10.3390/pathogens9121070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g−1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures.
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Affiliation(s)
- Anna Czubatka-Bieńkowska
- Department of Vegetable and Ornamental Plants Protection, Research Institute of Horticulture, Kościuszki 2, 96-100 Skierniewice, Poland; (A.C.-B.); (A.C.)
| | - Joanna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland;
| | - Katarzyna Marzec-Schmidt
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Gråbrödragatan19, 532 31 Skara, Sweden;
| | - Anna Nieróbca
- Department of Agriculture, Pope John Paul II State School of Higher Education, ul. Sidorska 95/97, 21-500 Biała Podlaska, Poland;
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24‑100 Puławy, Poland
| | - Agnieszka Czajka
- Department of Vegetable and Ornamental Plants Protection, Research Institute of Horticulture, Kościuszki 2, 96-100 Skierniewice, Poland; (A.C.-B.); (A.C.)
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland;
- Correspondence: ; Tel.: +48-61-655-0271
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Zhang YJ, Hou JX, Zhang S, Hausner G, Liu XZ, Li WJ. The intronic minisatellite OsMin1 within a serine protease gene in the Chinese caterpillar fungus Ophiocordyceps sinensis. Appl Microbiol Biotechnol 2016; 100:3599-610. [PMID: 26754819 DOI: 10.1007/s00253-016-7287-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 12/01/2022]
Abstract
Repetitive DNA sequences make up a significant portion of all genomes and may occur in intergenic, regulatory, coding, or even intronic regions. Partial sequences of a serine protease gene csp1 was previously used as a population genetic marker of the Chinese caterpillar fungus Ophiocordyceps sinensis, but its first intron region was excluded due to ambiguous alignment. Here in this study, we report the presence of a minisatellite OsMin1 within this intron, where a 20(19)-bp repeat motif is duplicated two to six times in different isolates. Fourteen intron alleles and 13 OsMin1 alleles were identified among 125 O. sinensis samples distributed broadly on the Tibetan Plateau. Two OsMin1 alleles were prevalent, corresponding to either two or five repeats of the core sequence motif. OsMin1 appears to be a single locus marker in the O. sinensis genome, but its origin is undetermined. Abundant recombination signals were detected between upstream and downstream flanking regions of OsMin1, suggesting that OsMin1 mutate by unequal crossing over. Geographic distribution, fungal phylogeny, and host insect phylogeny all significantly affected intron distribution patterns but with the greatest influence noted for fungal genotypes and the least for geography. As far as we know, OsMin1 is the first minisatellite found in O. sinensis and the second found in fungal introns. OsMin1 may be useful in designing an efficient protocol to discriminate authentic O. sinensis from counterfeits.
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Affiliation(s)
- Yong-Jie Zhang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Jun-Xiu Hou
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China
| | - Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, China
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Xing-Zhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wen-Jia Li
- Sunshine Lake Pharma Co., LTD, Dongguan, 523808, China
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Oliveira GAF, Dantas JLL, Oliveira EJ. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya. Genetica 2015; 143:613-31. [PMID: 26280323 DOI: 10.1007/s10709-015-9860-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
Abstract
The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.
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Affiliation(s)
- G A F Oliveira
- Universidade Federal do Recôncavo da Bahia (UFRB), Cruz das Almas, BA, Brazil
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Delourme R, Bousset L, Ermel M, Duffé P, Besnard AL, Marquer B, Fudal I, Linglin J, Chadœuf J, Brun H. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape. INFECTION GENETICS AND EVOLUTION 2014; 27:490-9. [PMID: 24394446 DOI: 10.1016/j.meegid.2013.12.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/20/2013] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
Abstract
Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.
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Affiliation(s)
- R Delourme
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
| | - L Bousset
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
| | - M Ermel
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
| | - P Duffé
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
| | - A L Besnard
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
| | - B Marquer
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
| | - I Fudal
- INRA, UR 1290 BIOGER, BP 01, F-78850 Thiverval-Grignon, France.
| | - J Linglin
- INRA, UR 1290 BIOGER, BP 01, F-78850 Thiverval-Grignon, France.
| | - J Chadœuf
- INRA, UR 1052 GAFL, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France.
| | - H Brun
- INRA, UMR 1349 IGEPP, BP35327, F-35653 Le Rheu Cedex, France.
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Balesdent MH, Fudal I, Ollivier B, Bally P, Grandaubert J, Eber F, Chèvre AM, Leflon M, Rouxel T. The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. THE NEW PHYTOLOGIST 2013; 198:887-898. [PMID: 23406519 DOI: 10.1111/nph.12178] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/10/2013] [Indexed: 05/02/2023]
Abstract
Phytopathogenic fungi frequently contain dispensable chromosomes, some of which contribute to host range or pathogenicity. In Leptosphaeria maculans, the stem canker agent of oilseed rape (Brassica napus), the minichromosome was previously suggested to be dispensable, without evidence for any role in pathogenicity. Using genetic and genomic approaches, we investigated the inheritance and molecular determinant of an L. maculans-Brassica rapa incompatible interaction. Single gene control of the resistance was found, while all markers located on the L. maculans minichromosome, absent in the virulent parental isolate, co-segregated with the avirulent phenotype. Only one candidate avirulence gene was identified on the minichromosome, validated by complementation experiments and termed AvrLm11. The minichromosome was frequently lost following meiosis, but the frequency of isolates lacking it remained stable in field populations sampled at a 10-yr time interval, despite a yearly sexual stage in the L. maculans life cycle. This work led to the cloning of a new 'lost in the middle of nowhere' avirulence gene of L. maculans, interacting with a B. rapa resistance gene termed Rlm11 and introgressed into B. napus. It demonstrated the dispensability of the L. maculans minichromosome and suggested that its loss generates a fitness deficit.
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Affiliation(s)
- Marie-Hélène Balesdent
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Pascal Bally
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Jonathan Grandaubert
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Frédérique Eber
- INRA, UMR1349 IGEPP, BP35327, F-35653, Le Rheu Cedex, France
| | | | - Martine Leflon
- CETIOM, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
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Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans. Fungal Biol 2011; 115:649-59. [DOI: 10.1016/j.funbio.2011.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 03/29/2011] [Accepted: 03/31/2011] [Indexed: 11/24/2022]
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Bally P, Grandaubert J, Rouxel T, Balesdent MH. FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets. BMC Res Notes 2010; 3:322. [PMID: 21114810 PMCID: PMC3002364 DOI: 10.1186/1756-0500-3-322] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 11/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro-and minisatellites are among the most powerful genetic markers known to date. They have been used as tools for a large number of applications ranging from gene mapping to phylogenetic studies and isolate typing. However, identifying micro-and minisatellite markers on large sequence data sets is often a laborious process. RESULTS FONZIE was designed to successively 1) perform a search for markers via the external software Tandem Repeat Finder, 2) exclude user-defined specific genomic regions, 3) screen for the size and the percent matches of each relevant marker found by Tandem Repeat Finder, 4) evaluate marker specificity (i.e., occurrence of the marker as a single copy in the genome) using BLAST2.0, 5) design minisatellite primer pairs via the external software Primer3, and 6) check the specificity of each final PCR product by BLAST. A final file returns to users all the results required to amplify markers. A biological validation of the approach was performed using the whole genome sequence of the phytopathogenic fungus Leptosphaeria maculans, showing that more than 90% of the minisatellite primer pairs generated by the pipeline amplified a PCR product, 44.8% of which showed agarose-gel resolvable polymorphism between isolates. Segregation analyses confirmed that the polymorphic minisatellites corresponded to single-locus markers. CONCLUSION FONZIE is a stand-alone and user-friendly application developed to minimize tedious manual operations, reduce errors, and speed up the search for efficient minisatellite and microsatellite markers departing from whole-genome sequence data. This pipeline facilitates the integration of data and provides a set of specific primer sequences for PCR amplification of single-locus markers. FONZIE is freely downloadable at: http://www.versailles-grignon.inra.fr/bioger/equipes/leptosphaeria_maculans/outils_d_analyses/fonzie.
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Affiliation(s)
- Pascal Bally
- Institut National de la Recherche Agronomique, UMR 1290 BIOGER, BP 01, Avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.
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Blaise F, Rémy E, Meyer M, Zhou L, Narcy JP, Roux J, Balesdent MH, Rouxel T. A critical assessment of Agrobacterium tumefaciens-mediated transformation as a tool for pathogenicity gene discovery in the phytopathogenic fungus Leptosphaeria maculans. Fungal Genet Biol 2007; 44:123-38. [PMID: 16979359 DOI: 10.1016/j.fgb.2006.07.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 07/11/2006] [Accepted: 07/13/2006] [Indexed: 10/24/2022]
Abstract
We evaluated the usefulness and robustness of Agrobacterium tumefaciens-mediated transformation (ATMT) as a high-throughput transformation tool for pathogenicity gene discovery in the filamentous phytopathogen Leptosphaeria maculans. Thermal asymmetric interlaced polymerase chain reaction allowed us to amplify the left border (LB) flanking sequence in 135 of 400 transformants analysed, and indicated a high level of preservation of the T-DNA LB. In addition, T-DNA preferentially integrated as a single copy in gene-rich regions of the fungal genome, with a probable bias towards intergenic and/or regulatory regions. A total of 53 transformants out of 1388 (3.8%) showed reproducible pathogenicity defects when inoculated on cotyledons of Brassica napus, with diverse altered phenotypes. Co-segregation of the altered phenotype with the T-DNA integration was observed for 6 of 12 transformants crossed. If extrapolated to the whole collection, this indicates that 1.9% of the collection actually corresponds to tagged pathogenicity mutants. The preferential insertion into gene-rich regions along with the high ratio of tagged mutants renders ATMT a tool of choice for large-scale gene discovery in L. maculans.
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Affiliation(s)
- Françoise Blaise
- Institut National de la Recherche Agronomique, Phytopathologie et Méthodologies de la Détection, Route de St-Cyr, F-78026 Versailles Cedex, France
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Goodwin SB, van der Lee TAJ, Cavaletto JR, Te Lintel Hekkert B, Crane CF, Kema GHJ. Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola. Fungal Genet Biol 2006; 44:398-414. [PMID: 17074520 DOI: 10.1016/j.fgb.2006.09.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 09/18/2006] [Accepted: 09/20/2006] [Indexed: 11/25/2022]
Abstract
A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species.
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Affiliation(s)
- Stephen B Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit, Department of Botany and Plant Pathology, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.
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Gout L, Eckert M, Rouxel T, Balesdent MH. Genetic variability and distribution of mating type alleles in field populations of Leptosphaeria maculans from France. Appl Environ Microbiol 2006; 72:185-91. [PMID: 16391041 PMCID: PMC1352181 DOI: 10.1128/aem.72.1.185-191.2006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Accepted: 10/03/2005] [Indexed: 11/20/2022] Open
Abstract
Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used.
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Affiliation(s)
- Lilian Gout
- Phytopathologie et Méthodologies de la Détection, INRA, Unité PMDV, Route de Saint Cyr, 78026 Versailles Cedex, France
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Hayden HL, Howlett BJ. Genetic structure of a population of the fungus Leptosphaeria maculans in a disease nursery of Brassica napus in Australia. Curr Genet 2005; 48:142-9. [PMID: 16032414 DOI: 10.1007/s00294-005-0006-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/10/2005] [Accepted: 06/12/2005] [Indexed: 10/25/2022]
Abstract
Microsatellite, minisatellite and mating type markers were used to determine the genetic structure of the fungus Leptosphaeria maculans within a disease nursery, where Brassica napus lines were screened for resistance to blackleg disease under high inoculum pressure. Fungal isolates were collected from pseudothecia in infected stubble and pycnidia within cotyledon lesions on seedlings within the nursery. Genetic diversity was high with gene diversity at H=0.700 across four polymorphic loci, and genotypic diversity at D=0.993. Among the 159 isolates analysed, 102 multilocus genotypes were identified. The even distribution of mating type idiomorphs MAT1-1 and MAT1-2 and gametic equilibrium within the population provided further evidence of random mating. Genetic diversity was distributed on a very fine scale in the disease nursery. The majority of genetic diversity (67%) was distributed among conidia within a lesion or among ascospores from a piece of stubble, while the remainder (33%) was distributed within lesions on seedlings or different stubble pieces. There were no among-group differences between samples from stubble and seedlings. This is consistent with the low level of genetic differentiation between the ascospore and conidia samples (F (ST)=0.017) indicating that all isolates of L. maculans from the disease nursery most likely belong to one population, and that ascospores form the primary inoculum in the disease nursery.
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Affiliation(s)
- Helen L Hayden
- School of Botany, The University of Melbourne, Melbourne, VIC 3010, Australia.
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Rouxel T, Balesdent MH. The stem canker (blackleg) fungus, Leptosphaeria maculans, enters the genomic era. MOLECULAR PLANT PATHOLOGY 2005; 6:225-41. [PMID: 20565653 DOI: 10.1111/j.1364-3703.2005.00282.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
UNLABELLED SUMMARY Leptosphaeria maculans is the most ubiquitous pathogen of Brassica crops, and mainly oilseed brassicas (oilseed rape, canola), causing the devastating 'stem canker' or 'blackleg'. This review summarizes our current knowledge on the pathogen, from taxonomic issues to specific life traits. It mainly illustrates the importance of formal genetics approaches on the pathogen side to dissect the interaction with the host plants. In addition, this review presents the main current research topics on L. maculans and focuses on the L. maculans genome initiative recently begun, including its main research issues. TAXONOMY Leptosphaeria maculans (Desm.) Ces. & de Not. (anamorph Phoma lingam Tode ex Fr.). Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes (Loculoascomycetes), Order Pleosporales, Genus Leptosphaeria, Species maculans. HOST RANGE cultivated Brassicas such as Brassica napus (oilseed rape, canola), B. rapa, B. juncea, B. oleracea, etc., along with numerous wild crucifers species. Arabidopsis thaliana was recently reported to be a potential host for L. maculans. Primary disease symptoms are greyish-green collapse of cotyledon or leaf tissue, without a visible margin, bearing tiny black spots (pycnidia). The fungus then develops an endophytic symptomless growth for many months. Secondary symptoms, at the end of the growing season, are dry necroses of the crown tissues with occasional blackening (stem canker or blackleg) causing lodging of the plants. Pseudothecia differentiate on leftover residues. Seedling damping-off and premature ripening are also reported under certain environmental conditions. USEFUL WEBSITES Leptosphaeria maculans sequencing project at Genoscope: http://www.genoscope.cns.fr/externe/English/Projets/Projet_DM/organisme_DM.html; the SECURE site: http://www.secure.rothamsted.ac.uk/ the 'Blackleg' group at the University of Melbourne: http://www.botany.unimelb.edu.au/blackleg/overview.htm.
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Affiliation(s)
- T Rouxel
- INRA-PMDV, Route de Saint Cyr, 78026 Versailles Cedex, France
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