Isolation and Characterization of 46 Novel Polymorphic EST-Simple Sequence Repeats (SSR) Markers in Two Sinipercine Fishes (Siniperca) and Cross-Species Amplification
With the development of next generation sequencing technologies, transcriptome level sequence collections are emerging as prominent resources for the discovery of gene-based molecular markers. In this study, we described the isolation and characterization of 46 novel polymorphic microsatellite loci for Siniperca chuatsi and Siniperca scherzeri from the transcriptome of their F 1 interspecies hybrids. Forty-three of these loci were polymorphic in S. chuatsi, and 20 were polymorphic in S. scherzeri. In S. chuatsi, the number of alleles per locus ranged from 2 to 8, and the observed and expected heterozygosities varied from 0.13 to 1.00 and from 0.33 to 0.85, respectively. In S. scherzeri, the number of alleles per locus ranged from 3 to 9, and the observed and expected heterozygosities varied from 0.19 to 1.00 and from 0.28 to 0.88, respectively. We also evaluated the cross-amplification of 46 polymorphic loci in four species of sinipercine fishes: Siniperca kneri, Siniperca undulata, Siniperca obscura, and Coreoperca whiteheadi. The interspecies cross-amplification rate was very high, totaling 94% of the 184 locus/taxon combinations tested. These markers will be a valuable resource for population genetic studies in sinipercine fishes.
References
[1]
Liang, Y.; Cui, X. The eco-physiological characteristics of artificial propagation in mandarin fish (Siniperca chuatsi). Acta Hydrobiol. Sin 1982, 16, 90–92.
[2]
Liu, J.; Cui, Y.; Liu, J. Food consumption and growth of two piscivorous fishes, the mandarin fish and the Chinese snakehead. J. Fish Biol 1998, 53, 1071–1083.
[3]
He, J.G.; Zeng, K.; Weng, S.P.; Chan, S.M. Experimental transmission, pathogenicity and physical-chemical properties of infectious spleen and kidney necrosis virus (ISKNV). Aquaculture 2002, 204, 11–24.
[4]
Zhang, C.; Zhao, Y. The resources status, recovery and reasonable utilization of Siniperca chuatsi in China (in Chinese). Bull. Biol 1999, 34, 9–11.
[5]
Walter, R.; Epperson, B.K. Geographic pattern of genetic variation in Pinus resinosa: Area of greatest diversity is not the origin of postglacial populations. Mol. Ecol 2001, 10, 103–111.
[6]
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.
[7]
Edwards, K.J.; Barker, J.H.; Daly, A.; Jones, C.; Karp, A. Microsatellite libraries enriched for several microsatellite sequences in plants. BioTechniques 1996, 20, 758–760.
[8]
Gupta, P.K.; Rustgi, S. Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct. Integr. Genomics 2004, 4, 139–162.
[9]
Saha, M.C.; Mian, M.A.; Eujay, I.; Zwonitzer, J.C.; Wang, L.; May, G.D. Tall fescue EST-SSR markers with transfer ability across several grass species. Theor. Appl. Genet 2004, 109, 783–791.
[10]
Zhang, B.; Li, Z.J.; Tong, J.G.; Liao, X.L. Isolation and characterization of 18 polymorphic microsatellite markers in Chinese mandarin fish Siniperca chuatsi (Basilewsky). Mol. Ecol. Notes 2006, 6, 1216–1218.
[11]
Kuang, G.Q.; Liu, Z.; Lu, S.Q.; Liu, H.Y.; Zhang, J.S.; Tang, J.Z. Isolation and characterization of microsatellite loci from Siniperca chuatsi (in Chinese). J. Fish Sci. China 2007, 14, 608–614.
[12]
Kuang, G.Q.; Liu, Z.; Lu, S.Q.; Liu, H.Y.; Zhang, J.S.; Xiao, T.Y. Isolation and characterization of microsatellite loci of Siniperca chuatsi from GenBank database (in Chinese). Acta Zool. Sin 2007, 53, 184–189.
[13]
Kuang, G.Q.; Lu, S.Q.; Zheng, S.M.; Wu, Q. Isolation and evaluation of 18 microsatellite loci in Siniperca chuatsi (Basilewsky). Mol. Ecol. Resour 2009, 9, 1473–1475.
[14]
Liu, X.L.; Luo, W.; Zeng, C.; Wang, W.M.; Gao, Z.X. Isolation of New 40 Microsatellite Markers in Mandarin Fish (Siniperca chuatsi). Int. J. Mol. Sci 2011, 12, 4180–4189.
[15]
Yang, M.; Liang, X.F.; Tian, C.X.; Gul, Y.; Dou, Y.Q.; Cao, L.; Yu, R. Isolation and characterization of fifteen novel microsatellite loci in golden mandarin fish (Siniperca scherzeri) Steindachne. Conserv. Genet. Resour 2012, doi:10.1007/s12686-012-9601-1.
[16]
Liu, H.Z. Studies on Skeleton Anatomy and Phylogeny of the Sinipericine Fishes. In Ph.D. Dissertation; Institute of Hydrobiology, Chinese Academy of Sciences: Wuhan, Hubei Province, 1993.
[17]
Barbara, T.; Palma-Silva, C.; Paggi, G.M.; Bered, F.; Fay, M.F.; Lexer, C. Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol. Ecol 2007, 16, 3759–3767.
[18]
Ellis, J.R.; Burke, J.M. EST-SSRs as a resource for population genetic analyses. Heredity 2007, 99, 125–132.
[19]
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, 400.
[20]
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 Bioinforma 2008, 9, 253.
[21]
National Center for Biotechnology Information, U.S. National Library of Medicine. Available online: http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome , accessed on 30 July 2012.
[22]
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.
[23]
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.
[24]
Raymond, M.; Rousset, F. GENEPOP (version 1.2): Population genetic software for exact tests and ecumenicism. J. Hered 1995, 86, 248–249.
