Comparative Transcriptome Analysis to Define Defense Responses in Brachypodium distachyon Induced by Puccinia graminis (f. sp. tritici, lolii, and phlei-pratensis)

Puccinia graminis is an obligate biotrophic fungus that causes stem rust, a serious disease of cereals and forage grasses. Some important formae speciales of P. graminis and their typical hosts are P. graminis f. sp. tritici (Pg-tr) in wheat and barley, P. graminis f. sp. lolii (Pg-lo) in perennial ryegrass and tall fescue, and P. graminis f. sp. phlei-pratensis (Pg-pp) in timothy grass. Brachypodium distachyon is a model to study temperate grasses and cereals. To assess the potential of the Brachypodium stem rust pathosystem for investigating molecular and genetic aspects of disease resistance, a collection of Brachypodium inbred lines was challenged with Pg-tr, Pg-lo or Pg-pp. The fungal isolate/Brachypodium line combinations demonstrated significant variation in stem rust resistance. Given the contrasting phenotypes obtained when inoculating with Pg-tr, Pg-lo or Pg-pp, line Bd1-1 was selected for further analyses. Histological analysis indicated that Pg-lo and Pg-pp are more efficient than Pg-tr in establishing a biotrophic interaction, and that Bd1-1 exhibits pre-haustorial resistance to Pg-tr and post-haustorial resistance to Pg-lo and Pg-pp. A comparative RNA-seq analysis of the early responses of Bd1-1 to Pg-lo, Pg-pp and Pg-tr was performed. Gene expression profiles were determined for two time points after inoculation, which captured the transcriptional events in response to appressorium formation (12 hpi, hours post-inoculation), and fungal penetration (18 hpi). Here, we present genes that displayed differential expression among the different fungal inoculations.