The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n = 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n = 20 and 2n = 30 cytotypes.

A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n ϭ 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.The past two decades have witnessed an explosion in the use of model eukaryotic organisms to aid studies on species of significant commercial or biological interest. Historically, specific eukaryotes (e.g. Saccharomyces cerevisiae and Caenorhabditis elegans) have attained the status of "models" because they reflect the individual characteristics of species of medical, industrial, or agricultural interest and are often small, easy to work with in large numbers, and cheap to maintain. More recently, the power of model species has been augmented by the development of whole genome sequencing programs. The new field of "functional genomics" provides further challenges for model organisms in the drive to understand the function of each gene in any genome. This requires a plethora of tools to allow an integrative examination of complex biological problems and relate phenotype to genotype. There are two distinct categories of technology that need to be in place to exploit fully any proposed model organism in a functional genomics program (Table I). The technology associated with "physical genomics" is often standardized, generally organism independent, and can be developed theoretically for any species, given sufficient investment of time and resources. In contrast, the "biological genomics" capability associated with any parti...

Grass crop genomics research frequently is hindered by large genome sizes and polyploidy. While rice is an attractive system for grass genomics due to its small genome size and available genome sequence, it is not particularly well-suited as a robust model system for all grass crops. The wild grass species Brachypodium distachyon (L.) P. Beauv. (Brachypodium) has recently gained favor as a new model system for grass crop genomics research because it possesses a suite of biological traits desired in a model system. Further, it is more closely related to the large and diverse group of cool season grass crops than is either rice (Oryza sativa L.) or sorghum [Sorghum bicolor (L.) Moench.], the second grass crop species whose genome has been sequenced. Thus, by virtue both of its biological attributes and its evolutionary history, Brachypodium fi lls an important gap in grass crop genomics research. A surge in interest in Brachypodium has led to rapid and signifi cant advances in the acquisition of knowledge and development of resources needed to exploit this species as a model system, including. the impending completion of a draft nuclear genome sequence of Brachypodium. Integration of diverse genetic and genomic resources developed or under development for Brachypodium with the genome sequence will encourage further adoption of this species as a bona fi de model plant system.Before 2001, the unassuming grass genus Brachypodium was perhaps more known for its enigmatic features such as the diversity of chromosome numbers in the genus (Robertson, 1981) and the proper placement of the genus in the evolutionary tree of the grass family Poaceae than for anything else (Catalan et al., 1995;Kellogg, 2001). However, at the end of 2001 a seminal paper was published that touted a member of this genus, Brachypodium distachyon (L.) P. Beauv. (referred to as Brachypodium throughout the rest of this paper), as a new model system for grass genomics (Draper et al., 2001). A compelling case was made in this publication for Brachypodium to be given consideration as a new model system for genomics. In particular, Brachypodium possesses the suite of traits desired in a model

SummaryIt is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box.