Communicated by G. Wenzel S. Naik · V. S. Gupta · P. K. Ranjekar ( ) Plant Molecular Biology Unit, Biochemical Sciences Division, National Chemical Laboratory, Pune, MS 411 008, India Tel.: #91-212-338234; 342779; Fax: #91-212-338234; 330233 E-mail: pkr@ems.ncl.res.in; vidya@ems.ncl.res.in K. S. Gill Department of Agronomy, University of Nebraska Lincoln, 362B Plant Sciences, P. O. Box 830915, Lincoln, Nebraska 68583-0915, USA V. S. Prakasa Rao · S. A. Tamhankar · S. Pujar Plant Sciences Division, Agharkar Research Institute, Agarkar Road, Pune, MS 411 004, India B. S. Gill Wheat Genetics Resource Center, Department of Plant Pathology Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506-5502, USA Theor Appl Genet (1998) 97 : 535—540  Springer-Verlag 1998 S. Naik · K. S. Gill · V. S. Prakasa Rao · V. S. Gupta S. A. Tamhankar · S. Pujar · B. S. Gill · P. K. Ranjekar Identification of a STS marker linked to the Aegilops speltoides -derived leaf rust resistance gene Lr28 in wheat Received: 20 February 1998 / Accepted: 4 March 1998 Abstract A sequence-tagged-site (STS) marker is re- ported linked to Lr28, a leaf rust resistance gene in wheat. RAPD (random amplified polymorphic DNA) analysis of near-isogenic lines (NILs) of Lr28 in eight varietal backgrounds was carried out using random primers. Genomic DNA enriched for low-copy se- quences was used for RAPD analysis to overcome the lack of reproducibility due to the highly repetitive DNA sequences present in wheat. Of 80 random primers tested on the enriched DNA, one RAPD marker distinguished the NILs and the donor parent from the susceptible recurrent parents. The additional band present in resistant lines was cloned, sequenced, and STS primers specific for Lr28 were designed. The STS marker (Indian patent pending: 380 Del98) was further confirmed by bulk segregation analysis of F  families. It was consistently present in the NILs, the resistant F  bulk and the resistant F  lines, but was absent in recurrent parents, the susceptible F  bulk and the susceptible F  lines. Key words RAPD · STS marker · Leaf rust resistance gene · Lr28 · Wheat Introduction The most common wheat rust, called leaf rust or brown rust, is caused by Puccinia recondita Rob. ex Desm. f. sp. tritici Ericks. & Henn, and occurs on the leaf blade and leaf sheath. Successful wheat production in areas of the world predisposed to rust continues to depend on the use of rust-resistant cultivars (Roelfs et al. 1992). During the last 2—3 decades much progress has been made in breeding for resistance to the disease. How- ever, due to a narrow genetic base and continuously evolving pathogen races, resistant varieties become sus- ceptible to the disease when grown in vast areas. One promising approach to overcome this problem is to develop a germplasm carrying combinations of several effective genes, especially those from wild relatives and related species, which can be successfully crossed with bread wheat (Jiang et al. 1994). So far, over 40 leaf rust (¸r) resistance genes have been identi- fied in wheat and related species and some of them have been introgressed into wheat (McIntosh et al. 1995). Bringing more than one gene together into a single elite variety by conventional means is very laborious and time consuming. In some cases it is not achievable because screening for one resistance gene interferes with the ability to screen for another, a frequent problem in disease resistance breeding, while in certain cases the virulent isolates for the resistant genes are not available. In recent years, DNA-based markers have shown great promise in expediting plant breeding procedures. The identification of molecular markers for resistance genes can efficiently facilitate the pyramiding of major genes into a valuable background in less time, making it more cost effective (Tanksley et al. 1989).