Brachypodium distachyon. A New Model System for Functional Genomics in Grasses

Abstract

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...

Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv.

“…The species of the genus Brachypodium have small chromosomes of variable number (x = 5, 7, 8, 9 or 10), making them unusual among the members of the Pooideae, which tend to have large chromosomes and base number of 7 (Shi et al 1993;Draper et al 2001;Hasterok et al 2004Hasterok et al , 2006Idziak and Hasterok 2008;Garvin et al 2008). Although ecotypes of B. distachyon with 10, 20 and 30 chromosomes have been described, some authors have indicated that these numbers do not represent a simple autopolyploid series (Robertson 1981).…”

“…Brachypodium is therefore seen as a ''bridge'' between rice and the Triticeae tribe. Various molecular phylogenetic analyses have shown that Brachypodium diverged from the ancestral stock of Pooideae immediately prior to the radiation of the modern ''core pooids'' (Catalan et al 1997;Catalan and Olmstead 2000;Draper et al 2001). It is also ancestral, but equally related to, Avena and Triticum (Kellogg 2001;Huo et al 2009).…”

“…distachyon has a rapid generation cycle under optimized conditions (8-12 weeks), does not grow very tall (20-30 cm) at high planting densities, requires few demanding growth resources, shows good environmental adaptation ) and the 2n = 10 forms do not require vernalization (Draper et al 2001;Ozdemir et al 2008;Vogel et al 2006). The species B. distachyon has been used to protect rural soils from erosion, especially in slope areas where water runoff, wind and other agents cause soil loss.…”

Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon

“…Brachypodium spp. is a useful model grass because of its small, completely sequenced diploid genome (International Brachypodium Initiative, 2010), simple growth requirements, large collection of accessions, inbreeding nature, and high rate of recombination (Draper et al, 2001;Vogel et al, 2006Vogel et al, , 2009Opanowicz et al, 2008;Filiz et al, 2009;Brkljacic et al, 2011;Huo et al, 2011;Mur et al, 2011). All of these characteristics make Brachypodium spp.…”

RNA interference for wheat functional gene analysis

“…These changes can alter the functional relationships between orthologous genes in wheat and rice, making it difficult to predict the function in one species based on the function of the orthologue in the other species. Brachypodium is emerging as a better model system for wheat because of the more recent divergence of these two lineages (35-40 million years) compared to the wheat-rice divergence (Draper et al 2001;Hasterok et al 2006;Vogel et al 2006). Although the successful sequencing of Brachypodium will most likely be a valuable resource for wheat, the first comparative genomic studies are showing multiple alterations of colinearity between these two genomes (Bossolini et al 2007;Valarik et al 2007) suggesting that a final validation of gene function directly in wheat will still be necessary.…”