Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.

Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.

A Latent Period Duration Model for Wheat Stem Rust.

Wheat stem rust (WSR), caused by Puccinia graminis subsp. graminis Pers., is a highly destructive disease of wheat and several other small grains. The discovery of P. graminis subsp. graminis race Ug99, which overcomes previously effective resistance in wheat, raises concerns for global wheat production and food security. There is currently no mathematical model that describes the duration of the WSR latent period based on temperature or heat units. A study using P. graminis subsp. graminis race GFCDC in 'Stephens' wheat was conducted at a range of temperatures (from 4.7 to 33.4°C), to determine their effect on latent period duration. There were significant differences in latent period duration among temperatures, and temperatures above 30°C generally were not conducive for pustule development. A mathematical model to predict latent period duration based on temperature was formulated; the model can be applied to data consisting of varying temperature readings measured at any desired time increment. The model was validated in outdoor experiments under natural conditions on Stephens and 'McNair' wheat. In field and outdoor experiments, the latent period durations predicted with the model were within 16 h of the observed latent period, and most fell into the 99% confidence interval of the observations. For experiments conducted on field-grown plants, no significant differences were found between predicted and observed latent period duration. Factorial experiments conducted under growth chamber conditions, using four wheat cultivars (Stephens, McNair 701, 'Scout 66', and 'Kingbird') and four P. graminis subsp. graminis races (GCCNC, GCCSC, QFCSC, and GFCDC) at three temperatures (5, 15 and 30°C) showed significant differences among cultivars at each temperature. A quantitative model for latent period duration could help in estimating epidemic development, and also in improving our understanding of WSR epidemiology.

Infection of Brachypodium distachyon by formae speciales of Puccinia graminis: early infection events and host-pathogen incompatibility.

Puccinia graminis causes stem rust, a serious disease of cereals and forage grasses. 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 an emerging genetic model to study fungal disease resistance in cereals and temperate grasses. We characterized the P. graminis-Brachypodium pathosystem to evaluate its potential for investigating incompatibility and non-host resistance to P. graminis. Inoculation of eight Brachypodium inbred lines with Pg-tr, Pg-lo or Pg-pp resulted in sporulating lesions later accompanied by necrosis. Histological analysis of early infection events in one Brachypodium inbred line (Bd1-1) indicated that Pg-lo and Pg-pp were markedly more efficient than Pg-tr at establishing a biotrophic interaction. Formation of appressoria was completed (60-70% of germinated spores) by 12 h post-inoculation (hpi) under dark and wet conditions, and after 4 h of subsequent light exposure fungal penetration structures (penetration peg, substomatal vesicle and primary infection hyphae) had developed. Brachypodium Bd1-1 exhibited pre-haustorial resistance to Pg-tr, i.e. infection usually stopped at appressorial formation. By 68 hpi, only 0.3% and 0.7% of the Pg-tr urediniospores developed haustoria and colonies, respectively. In contrast, development of advanced infection structures by Pg-lo and Pg-pp was significantly more common; however, Brachypodium displayed post-haustorial resistance to these isolates. By 68 hpi the percentage of urediniospores that only develop a haustorium mother cell or haustorium in Pg-lo and Pg-pp reached 8% and 5%, respectively. The formation of colonies reached 14% and 13%, respectively. We conclude that Brachypodium is an apt grass model to study the molecular and genetic components of incompatiblity and non-host resistance to P. graminis.

The use and role of predictive systems in disease management.

Disease predictive systems are intended to be management aids. With a few exceptions, these systems typically do not have direct sustained use by growers. Rather, their impact is mostly pedagogic and indirect, improving recommendations from farm advisers and shaping management concepts. The degree to which a system is consulted depends on the amount of perceived new, actionable information that is consistent with the objectives of the user. Often this involves avoiding risks associated with costly disease outbreaks. Adoption is sensitive to the correspondence between the information a system delivers and the information needed to manage a particular pathosystem at an acceptable financial risk; details of the approach used to predict disease risk are less important. The continuing challenge for researchers is to construct tools relevant to farmers and their advisers that improve upon their current management skill. This goal requires an appreciation of growers' decision calculus in managing disease problems and, more broadly, their overall farm enterprise management.