Abstract
An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.
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References
Akkaya MS, Shoemaker RC, Specht JE, Bhagwat AA, Cregan PB (1995) Integration of simple sequence repeat and markers into a soybean linkage map. Crop Sci 35:1439–1445
Hayden MJ, Stephenson P, Logojan AM, Khatkar D, Rogers C, Koebner RMD, Snape JW, Sharp PJ (2004) A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRs. Theor Appl Genet 108:733–742
Lian C, Hogetsu T (2002) Development of microsatellite markers in black locust (Robinia pseudoacacia) using a dual-suppression-PCR technique. Mol Ecol Notes 2:211–213
Lian CL, Zhou ZH, Hogetsu T (2001) A simple method for developing microsatellite markers using amplified fragments of inter-simple sequence repeat (ISSR). J Plant Res 114:381–385
Marshall TC, Slate J, Kruuk L, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Schuler GD, Boguski MS, Stewart EA et al (1996) A gene map of the human genome. Science 274:540–546
Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23:1087–1088
Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348
Valdes AM, Slatkin M, Freimer NB (1993) Allele frequencies at microsatellite loci—the stepwise mutation model revisited. Genetics 133:737–749
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Acknowledgments
This work was supported by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.
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Lian, C.L., Wadud, M.A., Geng, Q. et al. An improved technique for isolating codominant compound microsatellite markers. J Plant Res 119, 415–417 (2006). https://doi.org/10.1007/s10265-006-0274-2
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DOI: https://doi.org/10.1007/s10265-006-0274-2