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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #329216

Title: Molecular mapping of stem rust resistance loci effective against the Ug99 race group of the stem rust pathogen and identification of SNP marker linked to stem rust resistance gene Sr28

item Babiker, Ebrahiem
item Gordon, Tyler
item Chao, Shiaoman
item Rouse, Matthew
item ACEVEDO, MARICELIS - North Dakota State University
item WANYERA, RUTH - Kenya Agricultural And Livestock Research Organization
item Brown-Guedira, Gina
item Bonman, John

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2016
Publication Date: 2/9/2017
Citation: Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Acevedo, M., Wanyera, R., Brown Guedira, G.L., Bonman, J.M. 2017. Molecular mapping of stem rust resistance loci effective against the Ug99 race group of the stem rust pathogen and identification of SNP marker linked to stem rust resistance gene Sr28. Phytopathology. 107(2):208-215.

Interpretive Summary: A new race of the stem rust pathogen with virulence to the widely deployed stem rust resistance gene Sr31, originally designated as race TTKS and commonly referred to as ‘Ug99’, was reported in Uganda in 1999. The pathogen has continued to evolve and new races have emerged and overcome other widely deployed resistance genes, including Sr24, Sr36, and SrTmp. Due to the continued evolution of new races and the widespread susceptibility in wheat to Ug99, work is underway to explore the genetic variability present in the wheat landraces from the USDA-ARS National Small Grains Collection (NSGC) and identify resistance to Ug99. The spring wheat landrace accession PI 177906, showed resistance to Ug99 in field tests in Kenya. The objectives of this study were to elucidate the inheritance of Ug99 resistance in PI 177906 and map the seedling and field resistance using the recently developed wheat molecular markers, called single nucleotide polymorphisms (SNPs). The seedling screening indicating two loci controlled seedling resistance to Ug99. The SNP markers, were used to ‘genotype’ the populations of plants developed by crossing the resistant accessions PI 177906 with two susceptible lines. With this method we found that there are two major regions for Ug99 seedling and field resistance on chromosomes 2BL and 6DS. Based on race specificity and the mapping results, the Sr genes in PI 177906 were hypothesized to be one of the known genes Sr28 and either of Sr42 or SrTmp. We further used one of the SNP markers identified in this study and developed breeder-friendly SNP marker to be used to combine the Sr28 gene with other effective Sr genes. These results will help US wheat breeders develop new cultivars with better stem rust resistance.

Technical Abstract: Wheat landrace PI 177906 has field resistance to the Ug99 race group and seedling resistance to stem rust caused by Puccinia graminis f. sp. tritici (Pgt) races TTKSK, TTKST, and BCCBC. Two populations were developed from a cross between PI 177906 and LMPG-6, 138 double haploid (DH) lines and 140 recombinant inbred lines (RIL). Both populations were evaluated for seedling resistance to races TTKSK and BCCBC. Parents and the DH population were evaluated for field resistance in three seasons in Kenya. The 90K wheat iSelect SNP genotyping platform was used to genotype the parents and populations. Goodness-of-fit tests indicated that two dominant genes in PI 177906 conditioned seedling resistance to race TTKSK. Two major loci for seedling resistance were consistently mapped to the chromosome arms 2BL and 6DS in both populations. The BCCBC resistance in the two populations was mapped to the same location on chromosome arm 2BL as the TTKSK resistance. Using field data from the three seasons, two major QTL were consistently detected on the same regions on 2BL and 6DS. Based on the mapping result, race specificity, and the infection type observed in PI 177906, the TTKSK resistance on chromosome arm 2BL is likely due to Sr28 while the one on 6DS could be controlled by either Sr42, SrCad, or SrTmp. Using KASP assays, one SNP marker was found to be predictive for the presence of the TTKSK resistance locus in on chromosome arm 2BL and Sr28 suggesting the utility of this marker for marker-assisted-selection of Sr28.