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Identification and characterization of simple sequence repeat markers for Pythium aphanidermatum, P. cryptoirregulare, and P. irregulare and the potential use in Pythium population genetics

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Abstract

Six simple sequence repeat (SSR)-enriched genome libraries from Pythium aphanidermatum, P. irregulare, and P. cryptoirregulare were constructed to develop SSR markers. One hundred six SSR primer pairs for P. aphanidermatum, 73 for P. cryptoirregulare, and 82 for P. irregulare were initially identified. After examining primers, the most polymorphic and reproducible SSR markers were selected for each Pythium species; 14 in P. aphanidermatum, 21 in P. irregulare, and 22 in P. cryptoirregulare. Analysis of isolates from each Pythium species using SSR markers showed the high degree of gene diversity and polymorphic information content (PIC) value in the three species. The average number of alleles was 3.5–5.3 in the three Pythium species. Seven SSR loci from P. cryptoirregulare and P. irregualre showed the distinct genetic separations of P. irregualre complex isolates. SSR markers identified for the three Pythium target species were highly transferable to other closely related Pythium species. Cross-amplification was found in all SSR markers between P. cryptoirregulare and P. irregulare. SSR loci were successfully amplified by direct PCR from mycelia of P. aphanidermatum, P. cryptoirregulare, and P. irregulare. These newly developed SSR markers can be used for population genetic studies and monitoring the movement of isolates in crop production systems or in nature.

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Acknowledgments

This work was supported by the USDA-ARS Floriculture and Nursery Crops Research Initiative and The Pennsylvania State University Agricultural Experiment Station. We thank Rachel Leonard for her technical assistance throughout the study. We also thank Dr. Seogchan Kang, Dr. Maria Jimenez-Gasco, and Dr. Carla Garzón for their technical review and comments, and Dr. Seonghwan Kim for Pythium collections.

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  1. Department of Plant Pathology, The Pennsylvania State University, University Park, PA, 16802-4506, USA

    Seonghee Lee & Gary W. Moorman

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  1. Seonghee Lee
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  2. Gary W. Moorman
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Correspondence to Gary W. Moorman.

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Communicated by D. Ebbole.

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Lee, S., Moorman, G.W. Identification and characterization of simple sequence repeat markers for Pythium aphanidermatum, P. cryptoirregulare, and P. irregulare and the potential use in Pythium population genetics. Curr Genet 53, 81–93 (2008). https://doi.org/10.1007/s00294-007-0167-5

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  • DOI: https://doi.org/10.1007/s00294-007-0167-5

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