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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetics and Genomics for Improving Spring Wheat with Disease Resistance

Location: Plant Science Research

Title: Genome analysis of nonhost resistance to stem rust in Brachypodium

Author
item Garvin, David

Submitted to: Symposium Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: July 26, 2013
Publication Date: September 8, 2013
Citation: Garvin, D.F. 2013. Genome analysis of nonhost resistance to stem rust in Brachypodium [abstract]. 12th International Wheat Genetics Symposium, September 8-14, 2013, Yokohama, Japan. p. 59.

Technical Abstract: Wheat stem rust (WSR) caused by Puccinia graminis f. sp. tritici (Pgt) is considered to be the most damaging of the rusts. The new WSR isolate Ug99 which recently emerged in eastern Africa is virulent on the majority of the world’s wheat cultivars. The threat to global wheat production has driven much new research to develop wheat with Ug99 resistance. Most of the resistance derives from race-specific R genes. Reported adult plant stem rust resistance in wheat, presumed to be more durable, is likely due to QTLs. Nonhost resistance associated with microbial molecular pattern-triggered immunity is thought to be highly durable and may be exploited to develop resistance to stem rust that complements traditional genetical breeding approaches. We are employing the cool season model grass Brachypodium distachyon (Brachypodium) to dissect nonhost resistance to stem rust, including WSR. We previously documented natural variation for resistance both to P. graminis f. sp. phlei-pratensis (timothy stem rust, Pgpp) and to Pgt. To begin exploring the genetic and molecular basis of this natural variation, a recombinant inbred line (RIL) population segregating for Pgpp resistance was evaluated at the seedling stage, with results suggesting a single major gene for resistance. Illumina sequencing was conducted on pooled genomic DNA from 24 susceptible RILs, and the reads were mapped to the reference genome sequence of Bd21, the resistant parent of the population. Homozygous SNPs, called at 99% confidence, largely clustered in a 400 kb interval on one chromosome. To date, fine mapping of the gene in the population using markers designed from polymorphisms identified in the Illumina reads of the susceptible RIL pool has reduced the interval to approximately 91 kb, and we are mapping more markers to further refine the gene’s location. Interestingly, the interval appears to have no genes with homology to previously cloned disease resistance genes. We have developed additional populations from crosses between lines that exhibit differences in Pgt resistance, and are following a similar research pipeline to isolate nonhost resistance genes to Pgt in Brachypodium. Mutagenesis is providing further opportunities to dissect nonhost stem rust resistance in Brachypodium. Pools of EMS- and gamma ray-irradiated Brachypodium were screened with Pgpp, which identified both mutant classes exhibiting increased susceptibility and increased resistance, based on visual evaluation of disease phenotypes. Quantitative reverse transcription PCR confirmed that fungal biomass in infected tissues of these mutants was congruent with visual disease ratings. We now have identified additional putative mutants with altered resistance to Pgt. Segregating populations developed from crosses between the wildtype parents and select mutants are being used to initiate analyses of the causal mutations, using high throughput sequencing strategies similar to those employed to fine map the Pgpp resistance gene. Genes involved in wheat stem rust resistance that we isolate from the model plant Brachypodium not only will advance our understanding of nonhost resistance, but will also provide new resources for the molecular improvement of durable wheat stem rust resistance.

Last Modified: 8/1/2014
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