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Mohaimin AZ, Krishnamoorthy S, Shivanand P. A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield. Braz J Microbiol 2024; 55:587-628. [PMID: 38001398 PMCID: PMC10920616 DOI: 10.1007/s42770-023-01179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.
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Affiliation(s)
- Abdul Zul'Adly Mohaimin
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Sarayu Krishnamoorthy
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam.
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2
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Röhrs I, Linde M, Przetakiewicz J, Zelya A, Zelya G, Pucher A, Tlapák H, Debener T. Potato Wart Isolates from Europe and North America Form Distinct Clusters of Genetic Variation. Life (Basel) 2023; 13:1883. [PMID: 37763287 PMCID: PMC10532758 DOI: 10.3390/life13091883] [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: 08/01/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
We have extended previously published sets of simple sequence repeat markers for Synchytrium endobioticum, selected to be polymorphic for the German-standard isolates of pathotypes P1, P2, P6, P8, and P18. These markers also complement the extensive published information on DNA polymorphisms for the mitogenomes of Synchytrium endobioticum. This extended set of 35 markers representing 73 alleles differentiated 51 isolates from Europe and North America into three large, well-separated clusters and subclusters using dendrogram analysis, principal coordinates analysis (PCoA), and population substructure analysis using STRUCTURE 2.3.4 software. This suggests a limited number of introgressions of the wart disease pathogen into current potato growing areas, followed by recombination and admixture of populations through human activities. The new markers extend the published marker sets and are useful tools for future analyses of population structure and dynamics in Synchytrium endobioticum, which are necessary to understand the biology of the interaction between the pathogen and its potato host and to develop future control strategies.
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Affiliation(s)
- Ina Röhrs
- Institute for Plant Genetics, Leibniz University Hannover, 30419 Hanover, Germany; (I.R.); (M.L.)
| | - Marcus Linde
- Institute for Plant Genetics, Leibniz University Hannover, 30419 Hanover, Germany; (I.R.); (M.L.)
| | - Jaroslaw Przetakiewicz
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, Poland;
| | - Avrelia Zelya
- National Academy of Agrarian Sciences, Institute of Plant Protection, Ukrainian Scientific-Research Plant Quarantine Station, 60321 Boyany, Chernivtskiy Region, Ukraine
| | - George Zelya
- National Academy of Agrarian Sciences, Institute of Plant Protection, Ukrainian Scientific-Research Plant Quarantine Station, 60321 Boyany, Chernivtskiy Region, Ukraine
| | - Anna Pucher
- Institute for Plant Protection in Crops and Grassland, Julius Kühn-Institute, 14532 Kleinmachnow, Germany;
| | - Hana Tlapák
- Robert Koch-Institute, 13353 Berlin, Germany;
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz University Hannover, 30419 Hanover, Germany; (I.R.); (M.L.)
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Yan L, Li Y, Qing Y, Tao X, Wang H, Lai X, Zhang Y. Integrative Analysis of Genes Involved in the Global Response to Potato Wart Formation. FRONTIERS IN PLANT SCIENCE 2022; 13:865716. [PMID: 35845669 PMCID: PMC9277394 DOI: 10.3389/fpls.2022.865716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Synchytrium endobioticum, the causal agent of potato wart disease, poses a major threat to commercial potato production. Understanding the roles of transcriptionally regulated genes following pathogen infection is necessary for understanding the system-level host response to pathogen. Although some understanding of defense mechanisms against S. endobioticum infection has been gained for incompatible interactions, the genes and signaling pathways involved in the compatible interaction remain unclear. Based on the collection of wart diseased tubers of a susceptible cultivar, we performed phenotypic and dual RNA-Seq analyses of wart lesions in seven stages of disease progression. We totally detected 5,052 differentially expressed genes (DEGs) by comparing the different stages of infection to uninfected controls. The tendency toward differential gene expression was active rather than suppressed under attack by the pathogen. The number of DEGs step-up along with the development of the disease and the first, third and seventh of the disease stages showed substantially increase of DEGs in comparison of the previous stage. The important functional groups identified via Gene ontology (GO) and KEGG enrichment were those responsible for plant-pathogen interaction, fatty acid elongation and phenylpropanoid biosynthesis. Gene coexpression networks, composed of 17 distinct gene modules that contained between 25 and 813 genes, revealed high interconnectivity of the induced response and led to the identification of a number of hub genes enriched at different stages of infection. These results provide a comprehensive perspective on the global response of potato to S. endobioticum infection and identify a potential transcriptional regulatory network underlying this susceptible response, which contribute to a better understanding of the potato-S. endobioticum pathosystem.
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Affiliation(s)
- Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Liangshan, China
| | - Yan Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yuan Qing
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Liangshan, China
| | - Xiang Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Haiyan Wang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Liangshan, China
| | - Yizheng Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
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F H Strassert J, Rodríguez-Rojas A, Kuropka B, Krahl J, Kaya C, Pulat HC, Nurel M, Saroukh F, Radek R. Nephridiophagids (Chytridiomycota) reduce the fitness of their host insects. J Invertebr Pathol 2022; 192:107769. [PMID: 35597279 DOI: 10.1016/j.jip.2022.107769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022]
Abstract
Nephridiophagids are unicellular fungi (Chytridiomycota), which infect the Malpighian tubules of insects. While most life cycle features are known, the effects of these endobionts on their hosts remain poorly understood. Here, we present results on the influence of an infection of the cockroach Blattella germanica with Nephridiophaga blattellae (Ni = Nephridiophaga-infected) on physical, physiological, and reproductive fitness parameters. Since the gut nematode Blatticola blattae is a further common parasite of B. germanica, we included double infected cockroaches (N+Ni = nematode plus Ni) in selected experiments. Ni individuals had lower fat reserves and showed reduced mobility. The lifespan of adult hosts was only slightly affected in these individuals but significantly shortened when both Nephridiophaga and nematodes were present. Ni as well as N+Ni females produced considerably less offspring than parasite-free (P-free) females. Immune parameters such as the number of hemocytes and phenoloxidase activity were barely changed by Nephridiophaga and/or nematode infections, while the ability to detoxify pesticides decreased. Quantitative proteomics from hemolymph of P-free, Ni, and N+Ni populations revealed clear differences in the expression profiles. For Ni animals, for example, the down-regulation of fatty acid synthases corroborates our finding of reduced fat reserves. Our study clearly shows that an infection with Nephridiophaga (and nematodes) leads to an overall reduced host fitness.
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Affiliation(s)
- Jürgen F H Strassert
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Evolutionary and Integrative Ecology, Berlin, Germany.
| | - Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany; Internal Medicine - Vetmeduni Vienna, 1210 Vienna, Austria
| | - Benno Kuropka
- Protein Biochemistry, Institute of Chemistry and Biochemistry, Free University of Berlin, Berlin, Germany
| | - Joscha Krahl
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Cem Kaya
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Hakan-Can Pulat
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Mehmed Nurel
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Fatma Saroukh
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Renate Radek
- Evolutionary Biology, Institute of Biology, Free University of Berlin, Berlin, Germany.
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van de Vossenberg BTLH, Prodhomme C, Vossen JH, van der Lee TAJ. Synchytrium endobioticum, the potato wart disease pathogen. MOLECULAR PLANT PATHOLOGY 2022; 23:461-474. [PMID: 35029012 PMCID: PMC8916214 DOI: 10.1111/mpp.13183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Potato wart disease is considered one of the most important quarantine pests for cultivated potato and is caused by the obligate biotrophic chytrid fungus Synchytrium endobioticum. This review integrates observations from early potato wart research and recent molecular, genetic, and genomic studies of the pathogen and its host potato. Taxonomy, epidemiology, pathology, and formation of new pathotypes are discussed, and a model for molecular S. endobioticum-potato interaction is proposed. TAXONOMY Currently classified as kingdom: Fungi, phylum: Chytridiomycota, class: Chytridiomycetes, order: Chytridiales, family: Synchytriaceae, genus: Synchytrium, species: Synchytrium endobioticum, there is strong molecular support for Synchytriaceae to be transferred to the order Synchytriales. HOSTS AND DISEASE SYMPTOMS Solanum tuberosum is the main host for S. endobioticum but other solanaceous species have been reported as alternative hosts. It is not known if these alternative hosts play a role in the survival of the pathogen in (borders of) infested fields. Disease symptoms on potato tubers are characterized by the warty cauliflower-like malformations that are the result of cell enlargement and cell multiplication induced by the pathogen. Meristematic tissue on tubers, stolons, eyes, sprouts, and inflorescences can be infected while the potato root system seems to be immune. PATHOTYPES For S. endobioticum over 40 pathotypes, which are defined as groups of isolates with a similar response to a set of differential potato varieties, are described. Pathotypes 1(D1), 2(G1), 6(O1), and 18(T1) are currently regarded to be most widespread. However, with the current differential set other pathogen diversity largely remains undetected. PATHOGEN-HOST INTERACTION A single effector has been described for S. endobioticum (AvrSen1), which is recognized by the potato Sen1 resistance gene product. This is also the first effector that has been described in Chytridiomycota, showing that in this fungal division resistance also fits the gene-for-gene concept. Although significant progress was made in the last decade in mapping wart disease resistance loci, not all resistances present in potato breeding germplasm could be identified. The use of resistant varieties plays an essential role in disease management.
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Affiliation(s)
| | | | - Jack H. Vossen
- Plant BreedingWageningen University & ResearchWageningenNetherlands
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Totsky IV, Rozanova IV, Safonova AD, Batov AS, Gureeva YA, Khlestkina EK, Kochetov AV. Genotyping of potato samples from the GenAgro ICG SB RAS collection using DNA markers of genes conferring resistance to phytopathogens. Vavilovskii Zhurnal Genet Selektsii 2021; 25:677-686. [PMID: 34755022 PMCID: PMC8553976 DOI: 10.18699/vj21.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/19/2022] Open
Abstract
Wart (a disease caused by Synchytrium endobioticum) and golden cyst potato nematode (Globodera rostochiensis), which parasitize the roots of the host plant, cause signif icant damage to potato crop. Both of these disease factors are quarantined in the Russian Federation, and each registered variety is tested for resistance to their most common races and pathotypes. The main method of opposing such diseases is by the development of resistant varieties. An important step in this process is the selection of resistant genotypes from the population and the estimation of the resistance of hybrids obtained by crosses during the breeding process. Conducting a permanent phenotypic evaluation is associated with diff iculties, for example, it is not always possible to work with pathogens, and phenotypic evaluation is very costly and time consuming. However, the use of DNA markers linked to resistance genes can signif icantly speed up and reduce the cost of the breeding process. The aim of the study was to screen the GenAgro potato collection of ICG SB RAS using known diagnostic PCR markers linked to golden potato cyst nematode and wart resistance. Genotyping was carried out on 73 potato samples using three DNA markers 57R, CP113, Gro1-4 associated with nematode resistance and one marker, NL25, associated with wart resistance. The genotyping data were compared with the data on the resistance of the collection samples. Only the 57R marker had a high level of correlation (Spearman R = 0.722008, p = 0.000000, p < 0.05) between resistance and the presence of a diagnostic fragment. The diagnostic eff iciency of the 57R marker was 86.11 %. This marker can be successfully used for screening a collection, searching for resistant genotypes and marker-assisted selection. The other markers showed a low correlation between the presence of the DNA marker and resistance. The diagnostic eff iciency of the CP113 marker was only 44.44 %. Spearman's correlation coeff icient (Spearman R = -0.109218, p = 0.361104, p < 0.05) did not show signif icant correlation between resistance and the DNA marker. The diagnostic eff iciency of the NL25 marker was 61.11 %. No signif icant correlation was found between the NL25 marker and resistance (Spearman R = -0.017946, p = 0.881061, p < 0.05). The use of these markers for the search for resistant samples is not advisable.
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Affiliation(s)
- I V Totsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Rozanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A D Safonova
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Batov
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu A Gureeva
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E K Khlestkina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Li P, Fan R, Peng Z, Qing Y, Fang Z. Transcriptome analysis of resistance mechanism to potato wart disease. Open Life Sci 2021; 16:475-481. [PMID: 34027104 PMCID: PMC8122464 DOI: 10.1515/biol-2021-0045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 11/15/2022] Open
Abstract
To understand the molecular mechanism of the resistance to potato wart disease, we used the potato cultivar Qingshu 9 as the experimental material and prepared potato samples with different levels of disease through inoculation. The RNAs of the samples were extracted, and transcriptome analysis was performed on the samples not infected by the disease (control group) and also on the samples with different levels of disease, with the aid of high-throughput sequencing. Next, the differentially expressed genes (DEGs) associated with the resistance to potato wart disease were identified based on the analysis results. Using bioinformatic tools, the DEGs were functionally annotated, classified, and enriched in related metabolic pathways. The main results are as follows: Compared with the control group, 4 DEGs were identified in the samples with light disease, 52 were found in the samples with medium disease, and 214 were discovered in the samples with heavy disease. Potato mainly resists the wart disease by suppressing its gene expression, and the degree of suppression depends on the level of the disease; the disease resistance might be dominated by cellular nucleic acid-binding protein, AP2-like transcription factor, and E3 ubiquitin-protein ligase. This research provides new insights into the molecular mechanism of potato resistance against wart disease.
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Affiliation(s)
- Peihua Li
- College of Agronomy, Xichang Univeristy, Xichang, Sichuan 615013, China
| | - Ruihong Fan
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Zhengsong Peng
- College of Agronomy, Xichang Univeristy, Xichang, Sichuan 615013, China
| | - Yuan Qing
- College of Agronomy, Xichang Univeristy, Xichang, Sichuan 615013, China
| | - Zhirong Fang
- College of Agronomy, Xichang Univeristy, Xichang, Sichuan 615013, China
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Prodhomme C, van Arkel G, Plich J, Tammes JE, Rijk J, van Eck HJ, Visser RGF, Vossen JH. A Hitchhiker's guide to the potato wart disease resistance galaxy. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3419-3439. [PMID: 32918590 PMCID: PMC7567731 DOI: 10.1007/s00122-020-03678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/27/2020] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE Two novel major effect loci (Sen4 and Sen5) and several minor effect QTLs for potato wart disease resistance have been mapped. The importance of minor effect loci to bring full resistance to wart disease was investigated. Using the newly identified and known wart disease resistances, a panel of potato breeding germplasm and Solanum wild species was screened. This provided a state-of-the-art "hitch-hikers-guide" of complementary wart disease resistance sources. Potato wart disease, caused by the obligate biotrophic soil-born fungus Synchytrium endobioticum, is the most important quarantine disease of potato. Because of its huge impact on yield, the lack of chemical control and the formation of resting spores with long viability, breeding for resistant varieties combined with strict quarantine measures are the only way to efficiently and durably manage the disease. In this study, we set out to make an inventory of the different resistance sources. Using a Genome-Wide Association Study (GWAS) in the potato breeding genepool, we identified Sen4, associated with pathotypes 2, 6 and 18 resistance. Associated SNPs mapped to the south arm of chromosome 12 and were validated to be linked to resistance in one full-sib population. Also, a bulked segregant analysis combined with a Comparative Subsequence Sets Analysis (CoSSA) resulted in the identification of Sen5, associated with pathotypes 2, 6 and 18 resistance, on the south arm of chromosome 5. In addition to these two major effect loci, the GWAS and CoSSA allowed the identification of several quantitative trait loci necessary to bring full resistance to certain pathotypes. Panels of varieties and Solanum accessions were screened for the presence of Sen1, Sen2, Sen3, Sen4 and Sen5. Combined with pedigree analysis, we could trace back some of these genes to the ancestral resistance donors. This analysis revealed complementary resistance sources and allows elimination of redundancy in wart resistance breeding programs.
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Affiliation(s)
- Charlotte Prodhomme
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- FN3PT/Inov3PT, INRAE Keraiber, 29260, Ploudaniel, France
| | - Gert van Arkel
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Jarosław Plich
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR‑PIB), Młochów Research Center, Platanowa 19, 05‑831, Młochów, Poland
| | - Jasper E Tammes
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Averis Seeds B.V., Valtherblokken Z40, 7876 TC, Valthermond, The Netherlands
| | - Johan Rijk
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Pop Vriend Seeds B.V., Middenweg 52, 1619 BN, Andijk, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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Prodhomme C, Vos PG, Paulo MJ, Tammes JE, Visser RGF, Vossen JH, van Eck HJ. Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1859-1871. [PMID: 32043234 PMCID: PMC7237394 DOI: 10.1007/s00122-020-03559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/28/2020] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance. Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease. This paper addresses the challenge to apply molecular markers in potato breeding. Although markers linked to Sen1 were published before, the identification of haplotype-specific single-nucleotide polymorphisms may result in marker assays with high diagnostic value. To identify hs-SNP markers, we performed a genome-wide association study (GWAS) in a panel of 330 potato varieties representative of the commercial potato gene pool. SNP markers significantly associated with pathotype 1 resistance were identified on chromosome 11, at the position of the previously identified Sen1 locus. Haplotype specificity of the SNP markers was examined through the analysis of false positives and false negatives and validated in two independent full-sib populations. This paper illustrates why it is not always feasible to design markers without false positives and false negatives for marker-assisted selection. In the case of Sen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium between Sen1 and flanking SNP markers. Sen1 appeared to be the main source of pathotype 1 resistance in potato varieties, but it does not explain all the resistance observed. Recombination and introgression breeding may have introduced new, albeit rare haplotypes involved in pathotype 1 resistance. The GWAS approach, in such case, is instrumental to identify SNPs with the best possible diagnostic value for marker-assisted breeding.
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Affiliation(s)
- Charlotte Prodhomme
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Peter G Vos
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- HZPC Research B.V., Roptawei 4, 9123 JB, Metslawier, The Netherlands
| | - Maria João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jasper E Tammes
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Averis Seeds B.V., Valtherblokken Z40, 7876 TC, Valthermond, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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van de Vossenberg BTLH, Prodhomme C, van Arkel G, van Gent-Pelzer MPE, Bergervoet M, Brankovics B, Przetakiewicz J, Visser RGF, van der Lee TAJ, Vossen JH. The Synchytrium endobioticum AvrSen1 Triggers a Hypersensitive Response in Sen1 Potatoes While Natural Variants Evade Detection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1536-1546. [PMID: 31246152 DOI: 10.1094/mpmi-05-19-0138-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synchytrium endobioticum is an obligate biotrophic fungus of division Chytridiomycota. It causes potato wart disease, has a worldwide quarantine status and is included on the Health and Human Services and United States Department of Agriculture Select Agent list. S. endobioticum isolates are grouped in pathotypes based on their ability to evade host resistance in a set of differential potato varieties. Thus far, 39 pathotypes are reported. A single dominant gene (Sen1) governs pathotype 1 (D1) resistance and we anticipated that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host. The S. endobioticum-specific secretome of 14 isolates representing six different pathotypes was screened for effectors specifically present in pathotype 1 (D1) isolates but absent in others. We identified a single AvrSen1 candidate. Expression of this candidate in potato Sen1 plants showed a specific hypersensitive response (HR), which cosegregated with the Sen1 resistance in potato populations. No HR was obtained with truncated genes found in pathotypes that evaded recognition by Sen1. These findings established that our candidate gene was indeed Avrsen1. The S. endobioticum AvrSen1 is a single-copy gene and encodes a 376-amino-acid protein without predicted function or functional domains, and is the first effector gene identified in Chytridiomycota, an extremely diverse yet underrepresented basal lineage of fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands
| | | | | | - Marga P E van Gent-Pelzer
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | | | - Balázs Brankovics
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jarosław Przetakiewicz
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, 05-870 Błonie, Warsaw, Poland
| | | | - Theo A J van der Lee
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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11
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van de Vossenberg BTLH, Warris S, Nguyen HDT, van Gent-Pelzer MPE, Joly DL, van de Geest HC, Bonants PJM, Smith DS, Lévesque CA, van der Lee TAJ. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. Sci Rep 2019; 9:8672. [PMID: 31209237 PMCID: PMC6572847 DOI: 10.1038/s41598-019-45128-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/09/2023] Open
Abstract
Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands.
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands.
| | - Sven Warris
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Hai D T Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P E van Gent-Pelzer
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - David L Joly
- Université de Moncton, 18 avenue Antonine-Maillet, Moncton, Canada
| | - Henri C van de Geest
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Donna S Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A J van der Lee
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
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12
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Bartkiewicz A, Chilla F, Terefe-Ayana D, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Flath K, Linde M, Debener T. Improved genetic resolution for linkage mapping of resistance to potato wart in monoparental dihaploids with potential diagnostic value in tetraploid potato varieties. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2555-2566. [PMID: 30159644 PMCID: PMC6244520 DOI: 10.1007/s00122-018-3172-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/27/2018] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE We achieved improved mapping resolution of the major wart resistance locus Xla-TNL containing also Sen1 in a dihaploid population using SNP data and developed additional markers with diagnostic value in tetraploid varieties. We analyzed a segregating monoparental dihaploid potato population comprising 215 genotypes derived from a tetraploid variety that is highly resistant to Synchytrium endobioticum pathotypes 18 and 6. The clear bimodal segregation for both pathotypes indicated that a major dominant resistance factor in a simplex allele configuration was present in the tetraploid donor genotype. Compared to that in previous analyses of the same tetraploid donor in conventional crosses with susceptible tetraploid genotypes, a segregation pattern with a reduced genetic complexity of resistance in dihaploids was observed here. Using the 12.8 k SolCAP SNP array, we mapped a resistance locus to the Xla-TNL region containing also Sen1 on potato chromosome 11. The improved mapping resolution provided by the monoparental dihaploids allowed for the localization of the genes responsible for the resistance to both pathotypes in an interval spanning less than 800 kbp on the reference genome. Furthermore, we identified eight molecular markers segregating without recombination to pathotype 18 and pathotype 6 resistance. Also, two developed markers display improved diagnostic properties in an independent panel of tetraploid varieties. Overall, our data provide the highest resolution mapping of wart resistance genes at the Xla-TNL locus thus far.
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Affiliation(s)
- Annette Bartkiewicz
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
- DHD-Consulting GmbH, Hildesheim, Germany
| | - Friederike Chilla
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
- Julius Kühn-Institut, Kleinmachnow, Germany
| | - Diro Terefe-Ayana
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
- Westhoff, Südlohn-Oeding, Germany
| | - Jens Lübeck
- SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany
| | | | - Eckhard Tacke
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany
| | | | | | - Marcus Linde
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany.
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13
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Plich J, Przetakiewicz J, Śliwka J, Flis B, Wasilewicz-Flis I, Zimnoch-Guzowska E. Novel gene Sen2 conferring broad-spectrum resistance to Synchytrium endobioticum mapped to potato chromosome XI. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2321-2331. [PMID: 30094457 PMCID: PMC6208938 DOI: 10.1007/s00122-018-3154-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/30/2018] [Indexed: 05/09/2023]
Abstract
Key message Sen2 gene for potato wart resistance, located on chromosome XI in a locus distinct from Sen1 , provides resistance against eight wart pathotypes, including the virulent ones important in Europe. Synchytrium endobioticum causes potato wart disease imposing severe losses in potato production, and as a quarantine pathogen in many countries, it results in lost trade markets and land for potato cultivation. The resistance to S. endobioticum pathotype 1(D1) is widespread in potato cultivars but new virulent pathotypes appear and the problem re-emerges. To characterize and map a new gene for resistance to potato wart, we used diploid F1 potato population from a cross of potato clone resistant to S. endobioticum pathotype 1(D1) and virulent pathotypes: 2(G1), 6(O1), 8(F1), 18(T1), 2(Ch1), 3(M1) and 39(P1) with a potato clone resistant to pathotype 1(D1) only. The 176 progeny clones were tested for resistance to eight wart pathotypes with a modified Glynne-Lemmerzahl method. Bimodal distributions and co-segregation of resistance in the population show that a single resistance gene, Sen2, underlies the resistance to eight pathotypes. Resistance to pathotype 1(D1) was additionally conferred by the locus Sen1 inherited from both parents. Sen2 was mapped to chromosome XI using DArTseq markers. The genetic and physical distances between Sen1 and Sen2 loci were indirectly estimated at 63 cM and 32 Mbp, respectively. We developed PCR markers co-segregating with the Sen2 locus that can be applied in marker-assisted selection of potatoes resistant to eight important pathotypes of S. endobioticum. Wide spectrum of the Sen2 resistance may be an indication of durability which can be enhanced by the pyramiding of the Sen2 and Sen1 loci as in 61 clones selected within this study.
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Affiliation(s)
- Jarosław Plich
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR-PIB), Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland.
| | - Jarosław Przetakiewicz
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR-PIB), 05-870, Radzików, Błonie, Poland
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR-PIB), Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Bogdan Flis
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR-PIB), Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR-PIB), Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Ewa Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute - National Research Institute (IHAR-PIB), Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
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14
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Zong Y, Song Q, Li C, Jin S, Zhang D, Wang Y, Qiu JL, Gao C. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat Biotechnol 2018; 36:nbt.4261. [PMID: 30272679 DOI: 10.1038/nbt.4261] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/25/2018] [Indexed: 02/07/2023]
Abstract
Base editors (BEs) have been used to create C-to-T substitutions in various organisms. However, editing with rat APOBEC1-based BE3 is limited to a 5-nt sequence editing window and is inefficient in GC contexts. Here, we show that a base editor fusion protein composed of Cas9 nickase and human APOBEC3A (A3A-PBE) converts cytidine to thymidine efficiently in wheat, rice and potato with a 17-nucleotide editing window at all examined sites, independent of sequence context.
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Affiliation(s)
- Yuan Zong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qianna Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dingbo Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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15
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van de Vossenberg BTLH, Brankovics B, Nguyen HDT, van Gent-Pelzer MPE, Smith D, Dadej K, Przetakiewicz J, Kreuze JF, Boerma M, van Leeuwen GCM, André Lévesque C, van der Lee TAJ. The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen. BMC Evol Biol 2018; 18:136. [PMID: 30200892 PMCID: PMC6131824 DOI: 10.1186/s12862-018-1246-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen. RESULTS We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence. CONCLUSIONS Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.
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Affiliation(s)
- Bart T. L. H. van de Vossenberg
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 Utrecht, CT Netherlands
| | - Hai D. T. Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P. E. van Gent-Pelzer
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
| | - Donna Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - Kasia Dadej
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Jarosław Przetakiewicz
- Plant Breeding and Acclimatization Institute, National Research Institute, 05-870 Blonie, Radzikow, Warsaw, Poland
| | - Jan F. Kreuze
- International Potato Centre, Avenida La Molina, 1895 Lima, Peru
| | - Margriet Boerma
- Hilbrands Laboratorium BV, Kampsweg 27, 9418 PD Wijster, Wijster, The Netherlands
| | - Gerard C. M. van Leeuwen
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - C. André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A. J. van der Lee
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
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16
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Jeger M, Bragard C, Caffier D, Candresse T, Chatzivassiliou E, Dehnen-Schmutz K, Gilioli G, Grégoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Urek G, van Bruggen A, Van der Werf W, West J, Winter S, Vloutoglou I, Bottex B, Rossi V. Pest categorisation of Synchytrium endobioticum. EFSA J 2018; 16:e05352. [PMID: 32625985 PMCID: PMC7009611 DOI: 10.2903/j.efsa.2018.5352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Panel on Plant Health performed a pest categorisation of the fungus Synchytrium endobioticum, the causal agent of potato wart disease, for the European Union (EU). The identity of the pest is well established and reliable methods exist for its detection and identification. S. endobioticum is present in most continents. The pest is listed in Annex IAII of Directive 2000/29/EC and is present with a restricted and fragmentary distribution in the EU. The major host is Solanum tuberosum (potato), but in Mexico, the pest also affects wild Solanum spp. S. endobioticum could potentially enter the EU through multiple pathways associated with soil as substrate for non-host plants, contaminant or commodity. The presence of the pest in 16 EU Member States characterised by different climatic conditions suggests that it could establish in the rest of the EU. The disease induces the formation of warts on potato tubers, stolons and stem bases reducing plant growth and yield and making tubers unmarketable. Additional losses may occur during storage. The only available strategy to control the disease and prevent it from spreading is the application of strict phytosanitary measures and the cultivation of potato varieties resistant to the pathotype(s) present in the infested field(s). Specific phytosanitary measures exist (Council Directive 69/464/EEC) for the control of potato wart disease in the EU. The main uncertainties refer to the distribution and host range of the pest, and the importance of some pathways of entry. S. endobioticum meets all the criteria assessed by EFSA for consideration as potential Union quarantine pest. The criteria for considering S. endobioticum as a potential Union regulated non-quarantine pest are not met since, in addition to potato seed tubers, soil (as commodity, substrate or contaminant) and ware potato tubers are major means of spread.
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17
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van de Vossenberg B, Westenberg M, Adams I, Afanasenko O, Besheva A, Boerma M, Choiseul J, Dekker T, Flath K, van Gent-Pelzer M, Heungens K, Karelov A, Kibildiene I, Przetakiewicz J, Schlenzig A, Yakovleva V, van Leeuwen G. Euphresco Sendo: An international laboratory comparison study of molecular tests for Synchytrium endobioticum detection and identification. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2018; 151:757-766. [PMID: 31007393 PMCID: PMC6445494 DOI: 10.1007/s10658-017-1411-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 12/25/2017] [Indexed: 06/09/2023]
Abstract
An international test performance study (TPS) was organised to generate validation data for three molecular Synchytrium endobioticum tests: van den Boogert et al. (European Journal of Plant Pathology 113, 47-57, 2005), and van Gent-Pelzer et al. (European Journal of Plant Pathology, 126, 129-133, 2010) for the detection of S. endobioticum, and the pathotype 1(D1) identification test described by Bonants et al. (European Journal of Plant Pathology, 143, 495-506, 2015). Two TPS rounds were organised focussing on different test matrices, i.e. round 1: warted potato tissue, and round 2: resting spore suspensions. When using the tests for detection and identification of S. endobioticum in warted potato tissue, no significant differences were observed for diagnostic sensitivity, diagnostic specificity, overall accuracy, analytical sensitivity and robustness. When using the tests for detection and identification of S. endobioticum in resting spore suspensions, the van den Boogert and van Gent-Pelzer tests significantly outperform the Bonants test for diagnostic sensitivity and diagnostic specificity. For overall accuracy and analytical sensitivity, the van Gent-Pelzer significantly outperforms the van den Boogert and Bonants tests and is regarded as the test of choice when identifying S. endobioticum from resting spores. Tests regarded fit for purpose for routine testing of wart material and resting spore suspensions are proposed for the update of EPPO standard PM7/28(1) Synchytrium endobioticum.
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Affiliation(s)
- Bart van de Vossenberg
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands
| | - Marcel Westenberg
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands
| | - Ian Adams
- Fera Science Ltd., Sand Hutton, York, YO41 1LZ UK
| | - Olga Afanasenko
- All Russian Research Institute for Plant Protection, Podbelsky sh. 3, Pushkin, Saint Petersburg, Russia
| | - Ani Besheva
- Central laboratory for plant quarantine, 120, N. Moushanov Blvd, 1330 Sofia, Bulgaria
| | - Margriet Boerma
- Hilbrands Laboratorium BV, Kampsweg 27, 9418 PD Wijster, The Netherlands
| | - James Choiseul
- Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare Ireland
| | - Toos Dekker
- NAK, Randweg 14, 8304 AS Emmeloord, the Netherlands
| | - Kerstin Flath
- Julius Kühn-Institut, Stahnsdorfer Damm 81, 14532 Kleinmachnow, Germany
| | - Marga van Gent-Pelzer
- Wageningen Plant Research, BU Biointeractions & Plant Health, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kurt Heungens
- Institute for Agricultural and Fisheries Research, Plant Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Anatolii Karelov
- Institute of Plant Protection, 33 Vasylkivska Str, Kiev, 3022 Ukraine
| | - Ilona Kibildiene
- The State Plant Service, Phytosanitary Research Laboratory (Division), Ministry of Agriculture, Sukileliu str. 9A, LT - 11352 Vilnius, Lithuania
| | - Jaroslaw Przetakiewicz
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Alexandra Schlenzig
- Science and Advice for Scottish Agriculture, 1 Roddinglaw Road, Edinburgh, EH12 9FJ UK
| | - Vera Yakovleva
- All-Russian Plant Quarantine Center, Pogranichnaya 32, Bykovo, 140150 Ramenskoe region, Moscow, Oblast Russia
| | - Gerard van Leeuwen
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands
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18
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Busse F, Bartkiewicz A, Terefe-Ayana D, Niepold F, Schleusner Y, Flath K, Sommerfeldt-Impe N, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Linde M, Przetakiewicz J, Debener T. Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen. PHYTOPATHOLOGY 2017; 107:322-328. [PMID: 27827007 DOI: 10.1094/phyto-05-16-0197-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host-pathogen interactions in this difficult pathosystem. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Affiliation(s)
- Friederike Busse
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Annette Bartkiewicz
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Diro Terefe-Ayana
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Frank Niepold
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Yvonne Schleusner
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Kerstin Flath
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Nicole Sommerfeldt-Impe
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Jens Lübeck
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Josef Strahwald
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Eckhard Tacke
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Hans-Reinhard Hofferbert
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Marcus Linde
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Jarosław Przetakiewicz
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Thomas Debener
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
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Gagnon MC, van der Lee TAJ, Bonants PJM, Smith DS, Li X, Lévesque CA, Bilodeau GJ. Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data. PHYTOPATHOLOGY 2016; 106:636-644. [PMID: 26828229 DOI: 10.1094/phyto-12-15-0317-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.
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Affiliation(s)
- Marie-Claude Gagnon
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Theo A J van der Lee
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Peter J M Bonants
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Donna S Smith
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Xiang Li
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - C André Lévesque
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Guillaume J Bilodeau
- First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
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Obidiegwu JE, Sanetomo R, Flath K, Tacke E, Hofferbert HR, Hofmann A, Walkemeier B, Gebhardt C. Genomic architecture of potato resistance to Synchytrium endobioticum disentangled using SSR markers and the 8.3k SolCAP SNP genotyping array. BMC Genet 2015; 16:38. [PMID: 25887883 PMCID: PMC4407358 DOI: 10.1186/s12863-015-0195-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/31/2015] [Indexed: 11/20/2022] Open
Abstract
Background The soil borne, obligate biotrophic fungus Synchytrium endobioticum causes tumor-like tissue proliferation (wart) in potato tubers and thereby considerable crop damage. Chemical control is not effective and unfriendly to the environment. S. endobioticum is therefore a quarantined pathogen. The emergence of new pathotypes of the fungus aggravate this agricultural problem. The best control of wart disease is the cultivation of resistant varieties. Phenotypic screening for resistant cultivars is however time, labor and material intensive. Breeding for resistance would therefore greatly benefit from diagnostic DNA markers that can be applied early in the breeding cycle. The prerequisite for the development of diagnostic DNA markers is the genetic dissection of the factors that control resistance to S. endobioticum in various genetic backgrounds of potato. Results Progeny of a cross between a wart resistant and a susceptible tetraploid breeding clone was evaluated for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 most relevant in Europe. The same progeny was genotyped with 195 microsatellite and 8303 single nucleotide polymorphism (SNP) markers. Linkage analysis identified the multi-allelic locus Sen1/RSe-XIa on potato chromosome XI as major factor for resistance to all four S. endobioticum pathotypes. Six additional, independent modifier loci had smaller effects on wart resistance. Combinations of markers linked to Sen1/RSe-XIa resistance alleles with one to two additional markers were sufficient for obtaining high levels of resistance to S. endobioticum pathotypes 1, 2, 6 and 18 in the analyzed genetic background. Conclusions Potato resistance to S. endobioticum is oligogenic with one major and several minor resistance loci. It is composed of multiple alleles for resistance and susceptibility that originate from multiple sources. The genetics of resistance to S. endobioticum varies therefore between different genetic backgrounds. The DNA markers described in this paper are the starting point for pedigree based selection of cultivars with high levels of resistance to S. endobioticum pathotypes 1, 2, 6 and 18. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0195-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jude Eijkeme Obidiegwu
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany. .,National Root Crops Research Institute Umudike, PMB 7006, Umuahia, Abia State, Nigeria.
| | - Rena Sanetomo
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany. .,Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.
| | - Kerstin Flath
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Kleinmachnow, Germany.
| | | | | | - Andrea Hofmann
- Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany.
| | - Birgit Walkemeier
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany.
| | - Christiane Gebhardt
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany.
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Ansari MW, Tuteja N. Post-harvest quality risks by stress/ethylene: management to mitigate. PROTOPLASMA 2015; 252:21-32. [PMID: 25091877 DOI: 10.1007/s00709-014-0678-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/07/2014] [Indexed: 05/10/2023]
Abstract
Fresh produce, in actual fact, is exposed to multiple stresses through entire post-harvest phase such as handling, storage and distribution. The biotic stresses are associated with various post-harvest diseases leading to massive produce loss. Abiotic stresses such as drought, heat and chilling cause cell weakening, membrane leakage, flavour loss, surface pitting, internal browning, textural changes, softening and mealiness of post-harvest produce. A burst in 'stress ethylene' formation makes post-harvest produce to be at high risk for over-ripening, decay, deterioration, pathogen attack and physiological disorders. The mutation study of genes and receptors involved in ethylene signal transduction shows reduced sensitivity to bind ethylene resulting in delayed ripening and longer shelf life of produce. This review is aimed to highlight the various detrimental effects of stress/ethylene on quality of post-harvest produce, primarily fruits, with special emphasize to its subsequent practical management involving the 'omics' tools. The outcome of the literature appraised herein will help us to understand the physiological and molecular bases of stress/ethylene which sustain fruit quality at post-harvest phase.
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Affiliation(s)
- Mohammad W Ansari
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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