Development and characterization of EST-derived microsatellite makers for Manila clam ( Ruditapes philippinarum )
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TECHNICAL NOTE
Development and characterization of EST-derived microsatellite makers for Manila clam (Ruditapes philippinarum) Hong-Tao Nie • De-Peng Zhu • Feng Yang Li-Qiang Zhao • Xi-Wu Yan
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Received: 20 August 2013 / Accepted: 23 September 2013 / Published online: 4 October 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract Twenty-five polymorphic microsatellite makers were developed and characterized from expressed sequence tag sequence of the Manila clam, Ruditapes philippinarum. The number of alleles at each locus ranged from 3 to 20 with an average of seven alleles per locus. The observed and expected heterozygosity varied from 0.081 to 0.730 and from 0.127 to 0.926, respectively. Thirteen loci were found deviate significantly from Hardy–Weinberg equilibrium. These microsatellite loci will be useful for further studies on the population structure and genetic variation of this species. Keywords Ruditapes philippinarum Manila clam Microsatellite Polymorphism
The Manila clam, Ruditapes philippinarum, which is widely distributed on tidal flats in the West Pacific coasts from Russia to the Philippines, is one of the important commercial resources for the coastal fisheries. However, the wild stocks of R. philippinarum have been declining dramatically for last decades due to over-exploitation and the deterioration of environmental conditions in China. In recent years, recovery efforts such as artificial breeding program and stock enhancement are in progress (Zhang
H.-T. Nie D.-P. Zhu F. Yang L.-Q. Zhao X.-W. Yan (&) Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China e-mail: [email protected] H.-T. Nie Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
and Yan 2009). But, the genetic effects of hatchery individuals on wild populations of R. philippinarum have not yet been fully evaluated. Therefore, reasonable stock management and genetic improvement are required for sustainable development of R. philippinarum aquaculture industry. Microsatellites or simple sequence repeats (SSRs) have become one of most commonly used DNA markers in population genetics and evolutionary biology research, and they have been widely applied in studies of biological breeding, and genetic linkage maps. Although some microsatellite markers have been developed in R. philippinarum (Yasuda et al. 2007; An et al. 2009), more polymorphic microsatellites are still required in R. philippinarum to enable parentage, population genetics and genome mapping studies. In this study, we report 25 novel polymorphic microsatellite markers developed from expressed sequence tags (ESTs) of the R. philippinarum that will be useful for genetic research of this species. A total of 5,844 R. philippinarum ESTs obtained from GenBank (Sep 20, 2012) were scanned and assembled using SeqMan II sequence assembly software (DNASTAR Inc., Madison, WI) and 4,549 poten
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