Development of Genetic and Genomic Research Resources for Brachypodium distachyon, a New Model System for Grass Crop Research

Abstract

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

Brachypodium as an emerging model for cereal–pathogen interactions

“…As reviewed previously, brachypodium possesses characteristics required for an effective plant model, including small stature, self-fertilization (but able to be cross-fertilized), rapid generation time, a compact genome and high transformation efficiency (Garvin, 2008;Vogel and Bragg, 2009;Vain, 2011;Brkljacic et al, 2011).…”

Natural Variation of Flowering Time and Vernalization Responsiveness in Brachypodium distachyon

“…Brachypodium has a number of physical attributes that make it suitable for a model organism, such as a small genome, diploid strains, short life cycle, transformability, and small size [9][10][11]. In addition to a complete genome sequence, additional genetic and molecular resources include an expressed sequence tag and bacterial artificial chromosome libraries, microarrays, collections of natural strains, and the development of mutant populations (http:// www.brachypodium.org/).…”

“…1), but a vernalization treatment reduces this variability by reducing the time needed for winter-annual accessions to flower [10,11,15,16]. Information concerning the loci responsible for flowering-time differences in natural Brachypodium accessions is limited.…”

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).…”