ORIGINAL PAPER Q. J. Song Æ J. R. Shi Æ S. Singh Æ E. W. Fickus J. M. Costa Æ J. Lewis Æ B. S. Gill Æ R. Ward P. B. Cregan Development and mapping of microsatellite (SSR) markers in wheat Received: 17 August 2004 / Accepted: 1 November 2004 / Published online: 18 January 2005 Ó Springer-Verlag 2005 Abstract Microsatellite DNA markers are consistently found to be more informative than other classes of markers in hexaploid wheat. The objectives of this re- search were to develop new primers flanking wheat mi- crosatellites and to position the associated loci on the wheat genome map by genetic linkage mapping in the ITMI W7984 · Opata85 recombinant inbred line (RIL) population and/or by physical mapping with cytogenetic stocks. We observed that the efficiency of marker development could be increased in wheat by creating libraries from sheared rather than enzyme-digested DNA fragments for microsatellite screening, by focusing on microsatellites with the [ATT/TAA] n motif, and by adding an untemplated G-C clamp to the 5¢-end of primers. A total of 540 microsatellite-flanking primer pairs were developed, tested, and annotated from ran- dom genomic libraries. Primer pairs and associated loci were assigned identifiers prefixed with BARC (the acronym for the USDA-ARS Beltsville Agricultural Research Center) or Xbarc, respectively. A subset of 315 primer sets was used to map 347 loci. One hundred and twenty-five loci were localized by physical mapping alone. Of the 222 loci mapped with the ITMI popula- tion, 126 were also physically mapped. Considering all mapped loci, 126, 125, and 96 mapped to the A, B, and D genomes, respectively. Twenty-three of the new loci were positioned in gaps larger than 10 cM in the map based on pre-existing markers, and 14 mapped to the ends of chromosomes. The length of the linkage map was extended by 80.7 cM. Map positions were consistent for 111 of the 126 loci positioned by both genetic and physical mapping. The majority of the 15 discrepancies between genetic and physical mapping involved chro- mosome group 5. Introduction DNA markers are required for the creation of genetic maps that can be used to discover the position of genes or quantitative trait loci (QTLs) controlling important traits. The same markers can be used to incorporate genes and QTLs into improved cultivars via marker- assisted selection (MAS). Also, markers tightly linked to important genes provide the starting point for map- based cloning of those genes. In bread wheat, the restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) marker systems have detected only low levels of intraspecific polymorphism (Penner et al. 1995; Paull et al. 1998; Kim and Ward 2000; Hazen et al. 2002). In contrast, micro- satellite markers are consistently found to be highly polymorphic, easily visualized, stable, and co-dominant (Akkaya et al. 1992; Ro¨der et al. 1995; Powell et al. Electronic Supplementary Material Supplementary material is available for this article at http://dx.doi.org/10.1007/s00122-004- 1871-x Communicated by D. A. Hoisington Q. J. Song Æ E. W. Fickus Æ P. B. Cregan (&) Soybean Genomics and Improvement Lab, Beltsville Agricultural Research Center, USDA-ARS, MD 20705, USA E-mail: creganp@ba.ars.usda.gov Tel.: +1-301-5045070 Fax: +1-301-5045728 Q. J. Song Æ J. M. Costa Department of Natural Resource Sciences & Landscape Architecture, University of Maryland, MD 20742, USA J. R. Shi Æ J. Lewis Æ R. Ward Department of Crop and Soil Science, Michigan State University, East Lansing, MI 48824, USA Present address: J. R. Shi Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China S. Singh Æ B. S. Gill Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA Theor Appl Genet (2005) 110: 550–560 DOI 10.1007/s00122-004-1871-x