ORIGINAL PAPER H.-J. Lu Æ J.P. Fellers Æ T.L. Friesen S.W. Meinhardt Æ J.D. Faris Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs Received: 22 August 2005 / Accepted: 6 January 2006 / Published online: 3 February 2006 Ó Springer-Verlag 2006 Abstract The wheat Tsn1 gene confers sensitivity to the host-selective toxin Ptr ToxA produced by the tan spot fungus (Pyrenophora tritici-repentis). The long-term goal of this research is to isolate Tsn1 using a positional cloning approach. Here, we evaluated 54 ESTs (ex- pressed sequence tags) physically mapped to deletion bin 5BL 0.75–0.76, which is a gene-rich region containing Tsn1. Twenty-three EST loci were mapped as either PCR-based single-stranded conformational polymor- phism or RFLP markers in a low-resolution wheat population. The genetic map corresponding to the 5BL 0.75–0.76 deletion bin spans 18.5 cM and contains 37 markers for a density of 2 markers/cM. The EST-based genetic map will be useful for tagging other genes, establishing colinearity with rice, and anchoring se- quence ready BAC contigs of the 5BL 0.75–0.76 deletion bin. High-resolution mapping showed that EST-derived markers together with previously developed AFLP-de- rived markers delineated Tsn1 to a 0.8 cM interval. Flanking markers were used to screen the Langdon durum BAC library and contigs of 205 and 228 kb flanking Tsn1 were assembled, sequenced, and anchored to the genetic map. Recombination frequency averaged 760 kb/cM across the 228 kb contig, but no recombi- nation was observed across the 205 kb contig resulting in an expected recombination frequency of more than 10 Mb/cM. Therefore, chromosome walking within the Tsn1 region may be difficult. However, the sequenced BACs allowed the identification of one microsatellite in each contig for which markers were developed and shown to be highly suitable for marker-assisted selection of Tsn1. Introduction Tan spot, caused by fungus Pyrenophora tritici-repentis (Died.) Drechs, is an economically important disease of common wheat (Triticum aestivum L., 2n=6x=42, AABBDD genomes) and durum (T. turgidum L., 2n=4x=28, AABB genomes) in many wheat-growing areas throughout the world. Characteristic symptoms of this disease include tan necrosis and extensive chlorosis, which are genetically independent (Lamari and Bernier 1991). Severe disease during grain filling can result in significant yield losses because severe spotting reduces the photosynthetic area of the upper leaves. P. tritici-repentis races are known to produce host selective toxins (HSTs) that induce necrosis or chlorosis in sensitive wheat genotypes (DeWolfe et al. 1998). Ptr ToxA was the first HST produced by P. tritici-repentis to be described and well characterized (Toma´s and Bockus 1987; Ballance et al. 1989; Touri et al. 1995; Zhang et al. 1997). This toxin causes necrosis when infiltrated into leaves of sensitive wheat genotypes, while insensitive wheat genotypes have no reaction to the toxin. Insensi- tivity to Ptr ToxA is conditioned by a single recessive gene in wheat (Lamari and Bernier 1989), which has been designated tsn1 (Faris et al. 1996). Anderson et al. (1999) indicated that chromosome deletion lines without the tsn1 locus were also insensitive to Ptr ToxA. The Tsn1 allele was a major factor responsible for the symptom of tan necrosis in disease development, while Communicated by S. J. Knapp H.-J. Lu Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA J.P. Fellers USDA-ARS Plant Science and Entomology Research Unit, Kansas State University, Manhattan, KS 66506, USA T.L. Friesen Æ J.D. Faris (&) USDA-ARS Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Fargo, ND 58105, USA E-mail: farisj@fargo.ars.usda.gov Tel.: +1-701-2391339 Fax: +1-701-2391369 S.W. Meinhardt Department of Chemistry, North Dakota State University, Fargo, ND 58105, USA Theor Appl Genet (2006) 112: 1132–1142 DOI 10.1007/s00122-006-0215-4