Skip to main content
ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #343273

Title: Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat

item Yu, Long-Xi
item Chao, Shiaoman
item SINGH, RAVI - International Maize & Wheat Improvement Center (CIMMYT)
item SORRELLS, MARK - Cornell University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/28/2017
Publication Date: 2/27/2017
Publication URL:
Citation: Yu, L., Chao, S., Singh, R., Sorrells, M. 2017. Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat. PLoS One. doi: 10.1371/journal.pone.0171963.

Interpretive Summary: Wheat stem rust, caused by fungus pathogen Puccinia graminis f. sp. tritici, is one of the most destructive diseases of wheat. The emergence of new race of the pathogen named Ug99 (TTKSK, for North American nomination) and its derivatives in East Africa are virulent to many reported stem rust resistance genes. The Ug99 races are rapidly spreading throughout Africa and South Asia and threat to wheat production worldwide Developing durable and effective disease resistant wheat varieties is a high priority. Single Nucleotide Polymorphic (SNP) marker has become the marker of choice for MAS because of their high frequency, widespread distribution throughout the genome, and their suitability for high-throughput and automated genotyping. In the present study, we developed four SNP makers that linked to Sr25. These markers were validated in two populations containing 277 breeding lines using a high-throughput assay, named Kompetitive Allele Specific PCR (KASP). The result indicated that all of the four markers can identify Sr25 genotypes. The diagnostic ability of these markers provide a strategy for high throughput marker-assisted selection for Sr25 and can be beneficial in accelerating breeding programs to improve wheat resistance to stem rust such as Ug99.

Technical Abstract: Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat.