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Int. J. Mol. Sci. 2012, 13(11), 14946-14955; doi:10.3390/ijms131114946

Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification

1 Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China 2 Key Laboratory of Tarim Animal Husbandry Science and Technology, College of Animal Science, Tarim University, Alar 843300, China These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 21 September 2012 / Revised: 15 October 2012 / Accepted: 22 October 2012 / Published: 14 November 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The Ho ranged from 0.15 to 0.83, and He ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.
Keywords: Schizothorax biddulphi; PGM™ sequencing; microsatellite (SSR); polymorphism Schizothorax biddulphi; PGM™ sequencing; microsatellite (SSR); polymorphism
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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Luo, W.; Nie, Z.; Zhan, F.; Wei, J.; Wang, W.; Gao, Z. Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification. Int. J. Mol. Sci. 2012, 13, 14946-14955.

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