Association Mapping of Resistance to the Ug99 Race Group of the Stem Rust Pathogen in Winter Wheat Landraces

To identify new loci for resistance to the Ug99 race group of Puccinia graminis f. sp tritici (Pgt), an association mapping study was conducted with a panel of 285 winter wheat landraces genotyped with the 9K iSelect SNP genotyping platform. The panel was evaluated for seedling resistance to Pgt race TTKSK and for reaction to Ug99 in the field in Kenya for two seasons. Using a mixed linear model, two seedling resistance loci were detected on chromosome arms 2BL and 6DS. In the same chromosomal regions, Kenya field data revealed QTL on both chromosomes using 2012 data and on 2BL only using 2013 data. To verify the locations identified by the association mapping, bulk segregant analysis (BSA) was carried out on five F_2:3 populations developed by crossing five resistant accessions from the panel to a susceptible breeding line KS05WH14. In four populations, BSA located the TTKSK resistance on chromosome arm 2BL at a positional range of 104.3 – 112.5 cM on the wheat consensus map. Based on the map location, race specificity, and seedling infection type observed, the TTKSK resistance on 2BL could be due to Sr9h. In one population, BSA located the TTKSK resistance to chromosome 6DS arm in a region known to harbor Sr42, SrCad, and SrTmp.