Location: Cereal Crops ResearchTitle: Development and characterization of expressed sequence tag (EST)-derived microsatellite markers for the wheat stem rust fungus, Puccinia graminis f. sp. tritici) Author
Submitted to: APS Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 10/1/2008
Publication Date: 10/1/2008
Citation: Zhong, S., Leng, Y., Friesen, T.L., Faris, J.D., Szabo, L.J. 2008. Development and characterization of expressed sequence tag (EST)-derived microsatellite markers for the wheat stem rust fungus, Puccinia graminis f. sp. tritici. APS Annual Meeting. 98(6):S180 Interpretive Summary:
Technical Abstract: Puccinia graminis f. sp. tritici, the causal agent of stem rust in wheat, has caused devastating disease epidemics throughout history and is still posing a potential threat to wheat production in some regions of the world due to the appearance of new races. To develop microsatellite or simple sequence repeat (SSR) markers for population genetics studies, a total of 60,579 EST sequences (reads) generated from P. graminis f. sp tritici were screened for tandemly repeated di-and tri-nucleotide units using a bioinformatics approach, and 513 ESTs containing putative SSR loci with six or more repeat units were identified. Flanking primers were designed for 384 unique SSR loci, which mapped to different locations of the draft genome sequence of the fungus. These primers were tested for ampli'cation and polymorphism by PCR on twenty isolates of P. graminis f. sp. tritici from North America. Among the 384 primer pairs, 182 failed to produce PCR products, whereas 202 generated amplicons in at least two isolates. Seventy-two of the 202 primer pairs generated easily scored patterns with polymorphism among the isolates tested. Also, 101 primer pairs were found to show polymorphism between the two isolates CRL 78-21-BB463 and CRL 75-36-700-3 of P. graminis f. sp. tritici, which were used to generate a mapping population. The SSR loci were also amplified in the closely related rye stem rust fungus P. graminis f. sp. secalis. These SSR markers derived from ESTs will be useful for characterization of population structures and for gene mapping in P. graminis.