Next Article in Journal
Nec-1 Enhances Shikonin-Induced Apoptosis in Leukemia Cells by Inhibition of RIP-1 and ERK1/2
Previous Article in Journal
Fly Ash-based Geopolymer Lightweight Concrete Using Foaming Agent
Int. J. Mol. Sci. 2012, 13(6), 7199-7211; doi:10.3390/ijms13067199
Article

Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra

1
, 1
 and 2,*
Received: 7 May 2012; in revised form: 5 June 2012 / Accepted: 6 June 2012 / Published: 12 June 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
View Full-Text   |   Download PDF [202 KB, uploaded 19 June 2014]
Abstract: The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.
Keywords: Raja pulchra; pyrosequencing; microsatellite Raja pulchra; pyrosequencing; microsatellite
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


MDPI and ACS Style

Kang, J.-H.; Park, J.-Y.; Jo, H.-S. Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra. Int. J. Mol. Sci. 2012, 13, 7199-7211.

AMA Style

Kang J-H, Park J-Y, Jo H-S. Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra. International Journal of Molecular Sciences. 2012; 13(6):7199-7211.

Chicago/Turabian Style

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su. 2012. "Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra." Int. J. Mol. Sci. 13, no. 6: 7199-7211.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert