2011 Annual Report 1a.Objectives (from AD-416) 1) Identify candidate avirulence genes in the wheat leaf rust pathogen, Puccinia triticina, that may condition resistance to wheat leaf rust,. 2)Assemble association mapping population in hard winter wheat and analyze for resistance to leaf rust, stripe rust, and stem rust, and. 3)Construct and analyze mapping populations for resistance to wheat leaf rust, stripe rust, and stem rust. 1b.Approach (from AD-416) Candidate avirulence genes will be identified from gene expression studies or by analysis of genomic sequences of Puccinia triticina. Candidates will be tested for ability to induce hypersensitive necrotic responses on resistant wheat varieties. An association mapping population representing diverse hard winter wheat germplasm will be tested in the field and in the greenhouse for resistance to the three rusts. Lines will be genotyped using a large set of SNP markers. Genomic regions associated with lower mean disease scores will be further investigated. Mapping populations will be developed using the doubled haploid (DH) or the recombinant inbred line (RIL) approach for native and exotic sources of resistance to leaf rust, stripe rust, and stem rust. 3.Progress Report An association mapping population of U.S. hard winter wheat has been assembled and a second year of data on resistance to stripe rust in the field was collected. These data are currently being analyzed to identify genes that affect the infection type and severity of stripe rust. We also collected the first year of data on resistance to leaf rust. Recombinant inbred line mapping populations are under development for five sources of slow rusting resistance in several hard winter wheat backgrounds. Three of these are ready for phenotyping in the next cropping season. Crosses between resistant and susceptible hard winter wheat lines have been completed to create mapping populations for 20 sources of resistance to stripe rust. Effector genes are produced by pathogens and can trigger defense responses in the plant. Ten effector candidates were identified from a cDNA library made from haustoria (feeding structures) of the leaf rust pathogen. Three have been tested to determine if they induce a defense response in the plant. One of these, Pt27, triggers a reaction and appears to be an effector gene. We are currently verifying the results and looking for mutants to help test the hypothesis. The genotyping-by-sequencing (GBS) approach is now being applied to mapping Ug99 stem rust resistance genes in our program. We have generated GBS libraries for two of the goatgrass-derived stem rust mapping populations. We will use the GBS data on these two populations to identify markers closely linked with the resistance genes while making background selection for the recurrent parent genotype. This marker-assisted back-crossing approach will: . 1)identify molecular markers linked to stem rust resistance; and. 2)rapidly recover the elite wheat background for using these genes in breeding. We have also generated an F2 mapping population for the short segment of Sr39 and will use GBS to identify molecular markers for this alien introgression. Progress on this agreement is monitored by regularly discussing program goals and approaches and by reviewing annual accomplishments reports.