|Sakthikumar, Sharadha - Broad Institute Of Mit/harvard|
|Cuomo, Christina - Broad Institute Of Mit/harvard|
|Stoxen, Sam - University Of Minnesota|
|Pretorious, Zack - University Of The Free State|
Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 6/1/2010
Publication Date: 6/15/2010
Citation: Crouch, J., Sakthikumar, S., Cuomo, C., Stoxen, S., Pretorious, Z.A., Szabo, L.J. 2010. Application of Comparative Genomics for the Identification and Monitoring of the Highly Virulent African Race, Ug99, of Puccinia graminis [abstract]. Phytopathology. 100:S156.
Technical Abstract: Throughout human history, wheat stem rust caused by Puccinia graminis f.sp. tritici (Pgt) has been one of the most destructive diseases of cereal crops. Stem rust has been well controlled in the U.S. for nearly a half a century, but with the appearance of a new, highly virulent race of Pgt in Uganda ('Ug99'), this disease has reemerged as a serious threat to global food supplies. Ug99 has already spread throughout northeastern Africa, the Arabian Peninsula and recently into Central Asia, and is predicted to move into North America within 10 years, likely through human mediated activities. To date five members of the Ug99 lineage have been found in Africa, showing variation in virulence to the stem rust resistance genes Sr24, Sr31 and Sr36. Over 1 million SNPs were identified by mapping Illumina sequence data from five members of the Ug99 lineage as well as three additional isolates against the assembled Pgt reference genome. This SNP database was used to selectively design 38 real-time PCR hydrolysis probes, each containing at least two homozygous SNPs. By screening a worldwide collection of 270 Pgt isolates, we found that individually the probes were not capable of uniquely discriminating between Ug99 and other races. Nevertheless, when a suite of probes was used in combination, a distinct Ug99 fingerprint pattern was generated. Ultimately, this technology will be a key component in monitoring the movement of Ug99 through rapid and accurate identification.