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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Research Project #431353

Research Project: Genomic Analysis of Tan Spot Resistance in Wheat

Location: Cereal Crops Research

Project Number: 3060-21000-038-06-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2016
End Date: Aug 31, 2021

The objectives of this research project are to develop molecular markers suitable for marker-assisted selection against the tan spot susceptibility gene Tsc1, and to clone the Tsc1 gene using mutagenesis coupled with exome capture techniques.

Tan spot is a devastating foliar disease caused by a necrotrophic fungal pathogen and affects all classes of wheat. The wheat Tsc1 gene confers susceptibility to strains of the tan spot pathogen that produce the protein known as Ptr ToxC. Tsc1 has been shown to be widely distributed among all classes of wheat making it a major factor in disease susceptibility. The Tsc1 gene was previously mapped to the short arm of wheat chromosome 1A, but markers suitable for marker-assisted selection against Tsc1 have not been developed. To develop useful markers for Tsc1, two populations known to segregate for Tsc1 and hence reaction to Ptr ToxC-producing strains will be screened for reaction to tan spot caused by the isolate 331-9. One population is derived from a cross between LMPG-6 and PI 626573, and the other is derived from a cross between the wheat lines Penawawa and Louise. Both populations were previously genotyped with the wheat 9K SNP chip and whole genome maps have been assembled. Therefore, we will regress the tan spot reaction data onto the genotype data to locate the genomic region containing the Tsc1 gene. Next, additional SSR markers known to map to chromosome arm 1AS will be placed on the maps of both populations. To develop more markers, the contextual sequences of SNPs known to detect loci near the Tsc1 region but not yet placed in these populations will be used to identify corresponding wheat survey sequences. The wheat survey sequences will be interrogated for SSRs and other features to be used to develop additional user-friendly PCR-based markers. Finally, markers tightly linked to Tsc1 will be used to evaluate a set of diverse wheat genotypes to determine the robustness of the markers. The wheat line LMPG-6 will be treated with the chemical mutagen ethylmethane sulfonate to develop a population of mutants. The mutant population will be screened for reaction to tan spot caused by the isolate 331-9. Plants that show resistance to 331-9 will be considered candidates for Tsc1-disrupted mutants. DNA of the wild type LMPG-6 and of the Tsc1-disrupted mutant lines will be subjected to exome capture sequencing using an Illumina-based platform, and the sequence will be analyzed to identify the SNPs between the wild type and the mutants. Markers will be developed for the SNPs and mapped in the LMPG-6 x PI 626573 population to identify/confirm SNPs mapping to the Tsc1 locus. Candidate gene sequences will be identified using bioinformatics, and the candidates will be validated through re-evaluation of the mutant lines.