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Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs

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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 (expressed 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 polymorphism 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 sequence 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-derived 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 recombination 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.

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Acknowledgements

The authors thank Erik Doehler for technical support. The project was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number 2003-35300-13109 to J.D.F.

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Authors and Affiliations

  1. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105, USA

    H.-J. Lu

  2. USDA-ARS Plant Science and Entomology Research Unit, Kansas State University, Manhattan, KS , 66506, USA

    J.P. Fellers

  3. USDA-ARS Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Fargo, ND, 58105, USA

    T.L. Friesen & J.D. Faris

  4. Department of Chemistry, North Dakota State University, Fargo, ND , 58105, USA

    S.W. Meinhardt

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  1. H.-J. Lu
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  2. J.P. Fellers
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  3. T.L. Friesen
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  4. S.W. Meinhardt
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  5. J.D. Faris
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Correspondence to J.D. Faris.

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Communicated by S. J. Knapp

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Lu, HJ., Fellers, J., Friesen, T. et al. Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs. Theor Appl Genet 112, 1132–1142 (2006). https://doi.org/10.1007/s00122-006-0215-4

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  • DOI: https://doi.org/10.1007/s00122-006-0215-4

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