Development and characterization of 42 novel polymorphic microsatellite markers for Odontobutis potamophila from EST seq
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MICROSATELLITE LETTERS
Development and characterization of 42 novel polymorphic microsatellite markers for Odontobutis potamophila from EST sequences Lijuan Zhang • Hongwei Zhang • Yaping Zhang Fei Zhu • Xinyuan Hou • Yali Hu • Shaowu Yin
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Received: 17 November 2013 / Accepted: 25 December 2013 Springer Science+Business Media Dordrecht 2014
Abstract Expressed sequence tags (ESTs) are sources for microsatellite development. In this study, we isolated and characterized microsatellite makers for Odontobutis potamophila using next-generation sequencing. A total of 42 polymorphic microsatellite repeat markers were identified in 32 individuals from Dangtu wild population. The number of alleles per locus varied from 2 to 10, and the observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.061 to 0.878, respectively. These ESTSSR makers would provide sufficient polymorphism for population genetic studies, parentage and genome mapping of O. potamophila and its closely related fishes. Keywords Odontobutis potamophila Expressed sequence tags (EST) Microsatellites
Odontobutis potamophila is a small freshwater benthic fish mainly distributed in East Asia. It is an important aquaculture species in China because of its economic value, abundant natural resources and delicious flavor. In recent years, the wild resources of O. potamophila have seriously declined due to overfishing, environmental pollution and the rising demands for its production. Therefore, the genetic
L. Zhang H. Zhang Y. Zhang F. Zhu X. Hou Y. Hu S. Yin (&) Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China e-mail: [email protected] L. Zhang H. Zhang Y. Zhang F. Zhu X. Hou Y. Hu S. Yin Jiangsu Co-Innovation Center for Marine Bio-Industry Technology, Lianyungang 222005, China
conservation of O. potamophila is becoming essential for sustainable management of natural resources. The fish is listed as near threatened by IUCN (The International Union for the Conservation of Nature) in 2012 (Huckstorf 2012). Molecular markers are efficient tools for evaluating genetic resources and facilitate molecular maker-assisted breeding.Recently,expressed sequence tag (EST)-derived SSRs have been developed and are superior to genomic SSR. EST-SSRs associated with genes with known function are more useful for gene mapping (Gao et al. 2012) and construction of genetic maps in aquatic species. Herein, EST-SSR of O. potamophila was firstly reported. It would be useful tools for population genetic studies, as well as parentage and genome mapping of O. potamophila. A total of 40,905 EST sequences from a cDNA library of O. potamophila constructed in our lab.Microsatellite repeats using the MISA software (MicroSAtellite, http:// pgrc.ipk-gatersleben.de/misa). A total of 1,321 SSR loci were identified and 221 were selected for microsatellite marker optimization. Primers were designed with the PRIMER3 software (http://frodo.wi.mit.edu/cgi-bin/pri mer3/pr
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