We described and characterized 11 expressed sequence tag (EST)-derived simple sequence repeats (SSR) and seven genomic (G)-derived SSRs in Coreoperca whiteheadi Boulenger. The EST-SSRs comprised 62.2% di-nucleotide repeats, 32.2% tri-nucleotide repeats and 5.5% tetra-nucleotide repeats, whereas the majority of the G-SSRs were tri-nuleotide repeats (81.4%). The number of alleles for the 18 loci ranged from 3 to 6, with a mean of 3.8 alleles per locus. The observed (Ho) and expected heterozygosities (He) values ranged from 0.375 to 1.000, and 0.477 to 0.757, respectively. The polymorphic information content (PIC) values ranged from 0.466 to 0.706. The mean values number of alleles, Ho, He, and PIC of EST-SSRs were higher than those of the G-SSRs. Four microsatellite loci deviated signi？cantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction and no significant deviations in linkage disequilibrium (LD) were observed. These loci are the first to be characterized in C. whiteheadi and should be useful in the investigation of a genetic evaluation for conservation. Compared with 11 loci in C. whiteheadi, 37 potential polymorphic EST-SSRs were found in Siniperca chuatsi (Basilewsky), which will provide a valuable tool for mapping studies and molecular breeding programs in S. chuatsi.
References
[1]
Zhou, C.W.; Yang, Q.; Cai, D.L. On the classification and distribution of the sinipercinae fishes (family serranidae). Zool. Res 1988, 9, 113–125.
[2]
Liu, H.Z.; Chen, Y.Y. Phylogeny of the sinipercine fishes with some taxonomic notes. Zool. Res 1994, 15, 1–12.
[3]
Xiong, H.L.; Dai, J.J.; Chen, L. Study on anatomy structure of the digestive system of Coreoperca whiteheadi. J. Anhui Agri. Sci 2011, 39, 4015–4017.
[4]
Hamada, H.; Petrino, M.G.; Kakunaga, T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc. Natl. Acad. Sci. USA 1986, 79, 6465–6469.
[5]
Saha, M.C.; Cooper, J.D.; Rouf Mian, M.A.; Chekhovskiy, K.; May, G.D. Tall fescue genomic SSR markers: Development and transferability across multiple grass species. Theor. Appl. Genet 2006, 113, 1449–1458.
[6]
Zhao, W.G.; Lee, G.A.; Kwon, S.W.; Ma, K.H.; Lee, M.C.; Park, Y.J. Development and use of novel SSR markers for molecular genetic diversity in Italian millet (Setaria italica L.). Genes Genomics 2012, 34, 51–57.
[7]
Zane, L.; Bargelloni, L.; Patarnello, T. Strategies for microsatellite isolation: A review. Mol. Ecol 2002, 11, 1–16.
[8]
Li, Y.C.; Korol, A.B.; Fahima, T.; Nevo, E. Microsatellites within genes: Structure, function, and evolution. Mol. Biol. Evol 2004, 21, 991–1007.
[9]
Lu, X.; Wang, H.X.; Dai, P.; Liu, B.Z. Characterization of EST-SSR and genomic-SSR markers in the clam, Meretrix meretrix. Conserv. Genet. Resour 2011, 3, 655–658.
[10]
Miao, G.D.; Liu, H.W.; Ma, H.Y.; Chen, S.L.; Fan, T.J. Isolation and characterization of 54 polymorphic microsatellite loci for half-smooth Tongue Sole, Cynoglossus semilaevis. J. World Aquacult. Soc 2011, 42, 462–467.
[11]
Van Oosterhout, C.; Hutchinson, W.F.; Wills, D.P.M.; Shipley, P. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 2004, 4, 535–538.
[12]
Wang, X.W.; Luan, J.B.; Li, J.M.; Bao, Y.Y.; Zhang, C.X.; Liu, S.S. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 2010, 11, doi:10.1186/1471-2164-11-400.
[13]
Qu, C.M.; Liang, X.F.; Huang, W.; Cao, L. Isolation and characterization of 46 novel polymorphic EST-SSR markers in two sinipercine fishes (Siniperca) and cross-species amplification. Int. J. Mol. Sci 2012, 13, 9534–9544.
[14]
You, F.M.; Huo, N.; Gu, Y.Q.; Luo, M.C.; Ma, Y.; Hane, D.; Lazo, G.R.; Dvorak, J.; Anderson, O.D. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinf 2008, 9, doi:10.1186/1471-2105-9-253.
[15]
Li, Q.; Wan, J.M. SSRHUNTER: Development of a local searching software for SSR sites. Yichuan 2005, 27, 808–810.
[16]
Yeh, F.C.; Boyle, T.J.B. Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg. J. Bot 1997, 129, 157.
[17]
Botstein, D.; White, R.L.; Skolnick, M.; Davis, R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet 1980, 32, 314–331.
[18]
Raymond, M.; Rousset, F. GENEPOP (version 1.2): Population genetic software for exact tests and ecumenicism. J. Hered 1995, 86, 248–249.
