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Development of Expressed Sequence Tag-Drived Simple Sequence Repeat Markers and Diversity Analysis of Phytophthora capsici in China

Liu Pei-Qing, Wu Min-Liang, Li Ben-Jin, Lan Cheng-Zhong, Weng Qi-Yong, Chen Qing-He

Abstract


Phytophthora capsici is a highly dynamic and destructive pathogen of vegetable and great interests on the genetic structure of P. capsici have grown in the world. However, there is little genetic information about P. capsici based on the EST-SSR markers. In this study, 193 SSR markers were developed and 33 selected markers were successfully detected and they were polymorphic with the number of alleles per locus ranging from 2 to 7. 4 SSR markers were further selected for genetic diversity analysis and Nei’s genetic diversity values of 15 populations ranged from 0.38 to 0.66, with an average of 0.53. The higher polymorphism and greater transport ability of these markers among P. capsici species were proved by the expected heterozygosity (He =0.64) and Shannon’s index of diversity (I =1.14), indicating that they maintained a substantial level of genetic diversity. Additionally, the genetic differentiation among the 4 markers (Fst =0.15) was moderate and the gene flow among groups was consequent (Nm =1.69). Clustering analyses revealed that 15 populations are made of two differentiated genetic clusters and are similar regarding genetic diversity composition. Our results suggest that there are considerable evolutionary potential of P. capsici in China and useful management strategies should be adapt to it.

Keywords


Phytophthora capsici; expressed sequence tag (EST); simple sequence repeat (SSR); genetic diversity

References


Anderson, J., G. Churchill, J. Autrique, S. Tanksley and M. Sorrells. 1993. Optimizing parental selection for genetic linkage maps. Genome. 36: 181-186.

Baldwin, S., M. Pither-Joyce, K. Wright, L. Chen and J. McCallum. 2012. Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations. Mol. Breed. 30: 1401-1411.

Delgado, R., A. Monteros‐Altamirano, Y. Li, R. Visser, T. Lee and B. Vosman. 2013. Large subclonal variation in Phytophthora infestans populations associated with Ecuadorian potato landraces. Plant Pathol. 62: 1081–1088.

Hu, J.-b., X.-y. Zhou and J.-w. Li. 2010. Development of novel EST-SSR markers for cucumber (Cucumis sativus) and their transferability to related species. Sci. Hortic. 125: 534-538.

Jiao, Y., H.-m. Jia, X.-w. Li, M.-l. Chai, H.-j. Jia, Z. Chen, G.-y. Wang, C.-y. Chai, E. van de Weg and Z.-s. Gao. 2012. Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra). BMC genomics. 13: 201.

Kantety, R. V., M. La Rota, D. E. Matthews and M. E. Sorrells. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510.

Knapova, G. and U. Gisi. 2002. Phenotypic and genotypic structure of Phytophthora infestans populations on potato and tomato in France and Switzerland. Plant Pathol. 51: 641-653.

Lamour, K. and M. Hausbeck. 2001. Investigating the spatiotemporal genetic structure of Phytophthora capsici in Michigan. Phytopathology. 91: 973-980.

Lamour, K. H., R. Stam, J. Jupe and E. Huitema. 2012. The oomycete broad-host-range pathogen Phytophthora capsici. Mol. Plant Pathol.13: 329-337.

Li, P., S. Cao, Y. Dai, X. Li, D. Xu, M. Guo, Y. Pan and Z. Gao. 2012. Genetic diversity of Phytophthora capsici (Pythiaceae) isolates in Anhui Province of China based on ISSR-PCR markers. Genet. Mol. Res. 11: 4285-4296.

Lin, Y., J. Xu, X. Wang, X. Wu, Y. Li and Z. Zhu. 2008. Novel EST-SSR markers for genetic analysis of Phytophthora sojae. Sci. Agric. Sin. 41: 2294-2301.

Martin, F. N., Z. G. Abad, Y. Balci and K. Ivors. 2012. Identification and detection of Phytophthora: reviewing our progress, identifying our needs. Plant Dis. 96: 1080-1103.

McDonald, B. A. 1997. The population genetics of fungi: tools and techniques. Phytopathology. 87: 448-453.

McDonald, B. A. and C. Linde. 2002. Pathogen population genetics, evolutionary potential, and durable resistance. Annu. Rev. Phytopathol. 40: 349-379.

Moe, K. T., W. Zhao, H.-S. Song, Y.-H. Kim, J.-W. Chung, Y.-I. Cho, P. H. Park, H.-S. Park, S.-C. Chae and Y.-J. Park. 2010. Development of SSR markers to study diversity in the genus Cymbidium. Biochem. Syst. Ecol. 38: 585-594.

Papetti, C., J. M. Pujolar, M. Mezzavilla, M. La Mesa, J. Rock, L. Zane and T. Patarnello. 2012. Population genetic structure and gene flow patterns between populations of the Antarctic icefish Chionodraco rastrospinosus. J. Biogeogr. 39: 1361-1372.

Rohlf, F. J. 2002. NTSYS-pc. Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter Software, New York.

Silvar, C., F. Merino and J. Díaz. 2006. Diversity of Phytophthora capsici in Northwest Spain: analysis of virulence, metalaxyl response, and molecular characterization. Plant Dis. 90: 1135-1142.

Temnykh, S., G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour and S. McCouch. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452.

Thiel, T., W. Michalek, R. Varshney and A. Graner. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106: 411-422.

Wang, H., P. Huan, X. Lu and B. Liu. 2011. Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome. Genes Genet. Syst. 86: 197-205.

Wang, Z., D. B. Langston, A. S. Csinos, R. D. Gitaitis, R. R. Walcott and P. Ji. 2009. Development of an improved isolation approach and simple sequence repeat markers to characterize Phytophthora capsici populations in irrigation ponds in southern Georgia. Appl. Environ. Microbiol. 75: 5467-5473.

Yin, J., K. Jackson, B. Candole, A. Csinos, D. Langston and P. Ji. 2012. Aggressiveness and diversity of Phytophthora capsici on vegetable crops in Georgia. Ann. Appl. Biol. 160: 191-200.

Zhang, Z., Y. Li, H. Fan, Y. Wang and X. Zheng. 2006. Molecular detection of Phytophthora capsici in infected plant tissues, soil and water. Plant Pathol. 55: 770-775.

Zhao, Y., C. S. Prakash and G. He. 2012. Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database. BMC Res. notes. 5: 362.


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DOI: 10.33687/phytopath.002.03.0410

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Copyright (c) 2013 Liu Pei-Qing, Wu Min-Liang, Li Ben-Jin, Lan Cheng-Zhong, Weng Qi-Yong, Chen Qing-He

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