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      Population Dynamics of Phytophthora infestans in the Netherlands Reveals Expansion and Spread of Dominant Clonal Lineages and Virulence in Sexual Offspring

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          Abstract

          For a comprehensive survey of the structure and dynamics of the Dutch Phytophthora infestans population, 652 P. infestans isolates were collected from commercial potato fields in the Netherlands during the 10-year period 2000–2009. Genotyping was performed using 12 highly informative microsatellite markers and mitochondrial haplotypes. In addition, for each isolate, the mating type was determined. STRUCTURE analysis grouped the 322 identified genotypes in three clusters. Cluster 1 consists of a single clonal lineage NL-001, known as “Blue_13”; all isolates in this cluster have the A2 mating type and the Ia mitochondrial haplotype. Clusters 2 and 3 display a more elaborate substructure containing many unique genotypes. In Cluster 3, several distinct clonal lineages were also identified. This survey witnesses that the Dutch population underwent dramatic changes in the 10 years under study. The most notable change was the emergence and spread of A2 mating type strain NL-001 (or “Blue_13”). The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation and dispersal mechanism for successful genotypes. Isolates were also screened for absence of the Avrblb1/ipiO class I gene, which is indicative for virulence on Rpi-blb1. This is also the first report of Rpi-blb1 breakers in the Netherlands. Superimposing the virulence screening on the SSR genetic backbone indicates that lack the Avrblb1/ipiO class I gene only occurred in sexual progeny. So far, the asexual spread of the virulent isolates identified has been limited.

          Most cited references15

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          Arlequin (version 3.0): An integrated software package for population genetics data analysis

          Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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            POLYSAT: an R package for polyploid microsatellite analysis.

            We present an R package to help remedy the lack of software for manipulating and analysing autopolyploid and allopolyploid microsatellite data. POLYSAT can handle genotype data of any ploidy, including populations of mixed ploidy, and assumes that allele copy number is always ambiguous in partial heterozygotes. It can import and export genotype data in eight different formats, calculate pairwise distances between individuals using a stepwise mutation and infinite alleles model, estimate ploidy based on allele counts and estimate allele frequencies and pairwise F(ST) values. This software is freely available through the Comprehensive R Archive Network (http://cran.r-project.org/) and includes a thorough tutorial. © 2011 Blackwell Publishing Ltd.
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              Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight.

              Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating potato disease in the world. Control of late blight in the United States and other developed countries relies extensively on fungicide application. We previously demonstrated that the wild diploid potato species Solanum bulbocastanum is highly resistant to all known races of P. infestans. Potato germplasm derived from S. bulbocastanum has shown durable and effective resistance in the field. Here we report the cloning of the major resistance gene RB in S. bulbocastanum by using a map-based approach in combination with a long-range (LR)-PCR strategy. A cluster of four resistance genes of the CC-NBS-LRR (coiled coil-nucleotide binding site-Leu-rich repeat) class was found within the genetically mapped RB region. Transgenic plants containing a LR-PCR product of one of these four genes displayed broad spectrum late blight resistance. The cloned RB gene provides a new resource for developing late blight-resistant potato varieties. Our results also demonstrate that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                ggg
                ggg
                ggg
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                1 December 2012
                December 2012
                : 2
                : 12
                : 1529-1540
                Affiliations
                [* ]Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
                []Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
                []Laboratory of Plant Breeding, Wageningen University, 6708 PB Wageningen, The Netherlands
                [§ ]Laboratory of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
                [** ]Centre for BioSystems Biology, 6700 AB Wageningen, The Netherlands
                Author notes

                Supporting information is available online at http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004150/-/DC1.

                [1 ]Corresponding author: Plant Research International, P.O. Box 16, 6700AA Wageningen, The Netherlands. E-mail: theo.vanderlee@ 123456wur.nl
                Article
                GGG_004150
                10.1534/g3.112.004150
                3516475
                23275876
                3aa5cb51-01a9-4c4d-a6f0-9e1816a70a6b
                Copyright © 2012 Li et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 28 August 2012
                : 22 September 2012
                Categories
                Investigations
                Custom metadata
                v1

                Genetics
                late blight,blue_13,avirulence,microsatellites,population genetics
                Genetics
                late blight, blue_13, avirulence, microsatellites, population genetics

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