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Open AccessArticle

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

1
Biotechnology Research Division, NFRDI, Busan 619-705, Korea
2
Fisheries Resources and Environment Division, West Sea Fisheries Research Institute, NFRDI, Incheon 400-420, Korea
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2012, 13(6), 7199-7211; https://doi.org/10.3390/ijms13067199
Received: 7 May 2012 / Revised: 5 June 2012 / Accepted: 6 June 2012 / Published: 12 June 2012
(This article belongs to the Section Biochemistry)
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. View Full-Text
Keywords: Raja pulchra; pyrosequencing; microsatellite Raja pulchra; pyrosequencing; microsatellite
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. https://doi.org/10.3390/ijms13067199

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. https://doi.org/10.3390/ijms13067199

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. https://doi.org/10.3390/ijms13067199

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