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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #233209
Title: Development and characterization of expressed sequence tag (EST)-derived microsatellite markers for the wheat stem rust fungus, Puccinia graminis f.sp. tritici

Author
item ZHONG, SHAOBIN - NORTH DAKOTA STATE UNIV.
item LENG, YUEQIANG - NORTH DAKOTA STATE UNIV.
item Friesen, Timothy
item Faris, Justin
item Szabo, Les

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2008
Publication Date: 2/13/2009
Citation: Zhong, S., Leng, Y., Friesen, T.L., Faris, J.D., Szabo, L.J. 2009. Development and characterization of expressed sequence tag (EST)-derived microsatellite markers for the wheat stem rust fungus, Puccinia graminis f.sp. tritici. Phytopathology 99:282-289.

Interpretive Summary: Puccinia graminis f. sp. tritici is the causal agent of stem rust disease in wheat. The rust fungus has caused devastating disease epidemics throughout history and is still posing a threat to wheat production in some regions of the world due to the appearance of new races. A total of 60,579 EST sequences were used to develop molecular markers for use in population genetic studies. A total of 708 unisequences 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 in the genome. These primers were tested across nineteen isolates of the stem rust fungus as well as four isolates of closely related species. 202 of the 384 were useful for analysis. Seventy-two of the 202 primer pairs generated easily scored patterns with polymorphism among the isolates tested. Some of the SSR loci were also useful in other rust fungi that were tested. These SSR markers derived from ESTs will be useful for the characterization of population structure and for gene mapping in P. graminis.

Technical Abstract: Puccinia graminis f. sp. tritici is the causal agent of stem rust disease in wheat. The rust fungus 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 use in population genetic 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. A total of 708 unisequences 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 across nineteen isolates of P. graminis f. sp.tritici and four isolates of P. graminis f. sp. secalis from North America for amplification and polymorphism by PCR. 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. Some of the SSR loci were also amplified in several other rust fungi (P. triticina, P. hordei, and P. coronata f. sp. hordei) that were tested. These SSR markers derived from ESTs will be useful for the characterization of population structure and for gene mapping in P.graminis.