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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS, POPULATION BIOLOGY, AND HOST-PARASITE INTERACTIONS OF CEREAL RUST FUNGI AND THEIR DISEASES

Location: Cereal Disease Laboratory

Title: Sequencing Ug99 and Other Stem Rust Races: Progress and Results

Authors
item Szabo, Les
item Cuomo, Christina -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 15, 2009
Publication Date: March 17, 2009
Citation: Szabo, L.J., Cuomo, C. 2009. Sequencing Ug99 and Other Stem Rust Races: Progress and Results. BGRI Technical Workshop Proceedings. p. 20.

Technical Abstract: Over the last decade a number of different molecular methods have been used to characterize genetic diversity in Puccinia graminis. Multilocus DNA fingerprinting methods (AFLPs, RAPDs, SAMs and S-SAPs) have proven to be useful, but limited to phenotypic analysis due to the dikaryotic nature of rust fungi. More recently, locus-specific markers (SSRs) have been developed and used to characterize different races of P. graminis f. sp. tritici including Ug99. SSR analysis has demonstrated that Ug99 is distinct from common North American races as well as a select set of worldwide races. SSR analysis indicated that races TTKST and TTTSK from North Africa represent variants of TTKSK (Ug99), but was unable to distinguish between members of this lineage. The recent genome sequencing of a North American isolate of P. graminis f. sp. tritici provides a major opportunity for genetic analysis and development of rapid molecular methods for race analysis. The current assembly contains 392 scaffolds spanning 88.64 Mb and represents a consensus of the two haploid genomes (www.broad.mit.edu/annotation/genome/puccinia_graminis.3). Thirteen pairs of scaffolds have been identified that correspond to homologous regions of the two haploid genomes. Ug99 (05KEN156/04: 05KEN) was sequenced using Illumina technology as well as the isolate used for the original sequencing project (CRL 75-36-799-3: reference). Approximately, 21 million reads (1.6 gb) representing an average of 20X coverage was used in the analysis. Ninety seven percent of the genome was covered when reads from the reference isolate was aligned back against itself. In contrast, 79.6% of the reference genome was covered when the 05KEN reads were aligned indicating that approximately 18% of the reference genome is unique compared to the 05KEN isolate. In addition, only 41% of the 05KEN reads aligned to the reference genome as compared to 69.6% percent of the reference reads. The frequency of single nucleotide polymorphisms (SNPs) of the reference isolate was one SNP per 959 bases indicating a moderate level of polymorphism between the two haploid genomes. Comparing the 05KEN with the reference genome, the frequency of SNPs was 1 for every 212 bases indicating a high level of genetic diversity between these two isolates. Currently, the distribution of SNPs across the genome is being analyzed. The high level of genetic diversity between Ug99 and the North American reference genome is currently being exploited for the development of diagnostic assay for the rapid identification of Ug99 lineage.

Last Modified: 9/20/2014
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