Abstract
Next-generation Roche 454 pyrosequencing was used to rapidly identify polymorphic microsatellites from enriched DNA libraries for the pink stem borer, Sesamia inferens (Walker). A total of 1,459 simple sequence repeats (SSRs) were isolated from the microsatellite-enriched library using 454 sequencing. Thirty-nine microsatellite markers were selected to synthesize for further optimization, and 12 loci exhibited reliable amplification of a single product of expected size. The forward primer of 12 primer pairs was end labeled with a fluorescent dye. All of the 12 microsatellite loci were polymorphic, with 5–13 alleles per locus and observed heterozygosities ranging from 0.097 to 0.957. Here, we also tested these 12 SSRs for cross-species amplification in Chilo suppressalis (Walker), Tryporyza incertulas (Walker) and Cnaphalocrocis medinalis (Guenée). These polymorphic markers will be a valuable tool for analyses of population connectivity and genetic structure in this rice pest.
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References
Arthofer W, Steiner FM, Schlick-Steiner BC (2011) Rapid and cost-effective screening of newly identified microsatellite loci by high-resolution melting analysis. Mol Genet Genomics 286:225–235
Castoe TA, Poole AW, Gu W, Jason De Koning AP, Daza JM, Smith EN, Pollock DD (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour 10:341–347
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445
Excoffier L, Laval G, Schneider S (2005) ARLEQUIN (version. 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50
Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:361–372
Hammond RL, Saccheri IJ, Ciofi C, Coote T, Funk SM, Mcmillan WO, Bayes MK, Taylor E, Bruford MW (1998) Isolation of microsatellite markers in animals. In: Karp A, Isaac PG, Ingram DS (eds) Molecular tools for screening biodiversity. Chapman & Hall, London
IRRI (1996) International rice research institute Bt rice: research and policy. IRRI Information Series IRRI, Manila 5
Ishiguro N, Tsuchida K (2006) Polymorphic microsatellite loci for the rice stem borer, Chilo suppressalis (Walker) (Lepidoptera: Crambidae). Appl Entomol Zool 41:565–568
Karan M, Evans DS, Reilly D, Schulte K, Wright C, Innes D, Holton TA, Nikles DG, Dickinson GR (2012) Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. Mol Ecol Resour 12:344–353
Liu YD, Hou ML, Hao LX (2009) Twelve nuclear microsatellite loci for rice stem borer (Chilo suppressalis W.). Mol Ecol Resour 9:180–182
Malausa T, Gilles A, Meglecz E, Blanquart H, Duthoy S, Costedoat C, Dubut V, Pech N, Castagnone-Sereno P, Delye C, Feau N, Frey P, Gauthier P, Guillemaud T, Hazard L, Le Corre V, Lung-Escarmant B, Male PJ, Ferreira S, Martin JF (2011) High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Mol Ecol Resour 11:638–644
Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin JF (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26:403–404
Raymond M, Rousset F (1995) Genepop (Version 3.4): population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225
Singham GV, Vargo EL, Booth W, Othman AS, Lee CY (2012) Polymorphic microsatellite loci from an indigenous Asian fungus-growing termite, Macrotermes gilvus (Blattodea: Termitidae) and cross amplification in related taxa. Environ Entomol 41:426–431
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform 9:253
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Zhang DX, Hewitt GM (1998) Isolation of DNA from preserved specimens. In: Karp A, Isaac PG, Ingram DS (eds) Molecular tools for screening biodiversity: plants and animals. Chapman & Hall, London, pp 41–45
Zhu ZR, Cheng J, Zuo W, Lin XW, Guo YR, Jiang YP, Wu XW, Teng K, Zhai BP, Luo J, Jiang XH, Tang ZH (2007) Integrated management of rice stem borers in the yangtze Delta, China. In: Vreysen MJB, Robinson AS, Hendrichs J (eds) Area-wide control of insect pests:from research to field implementation. Springer, New York
Acknowledgments
This work was supported by the NSFC (National Natural Science Foundation of China, project nos. 31370439) and the 973 Projects Grant (2010CB951503) from the Ministry of Science and Technology of China.
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Yudi, L., Xingkui, A. & Maolin, H. Rapid microsatellite marker isolation for the Pink Stem Borer, Sesamia inferens (Lepidopetera: Noctuidae), through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries and cross amplification in related taxa. Appl Entomol Zool 49, 613–617 (2014). https://doi.org/10.1007/s13355-014-0286-7
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DOI: https://doi.org/10.1007/s13355-014-0286-7