Brachypodium: a new monocot model plant system emerges


  • David F Garvin

    Corresponding author
    1. USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN 55108, USA
    • USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN 55108, USA
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The small grass species Brachypodium distachyon (purple false brome) is potentially an ideal model plant system for grass crop research. To realise this potential, a range of genetic and genomic resources have been developed in a very short period of time, and more still are in the pipeline. David Garvin explains how these resources will establish B. distachyon as the newest model plant system and will fill a long-empty void in genomics resources for grass crop improvement. Copyright © 2007 Society of Chemical Industry

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Shoulder to shoulder: Brachypodium (right) may prove as useful as Arabidopsis (left)

Working grass hero

Early in 2006 the US Department of Energy (DOE) approved a project to sequence the nuclear genome of the wild grass species Brachypodium distachyon (Brachypodium); this project was coupled with an accompanying project to sequence nearly a quarter of a million expressed sequence tags (ESTs) from the same species ( It is expected that the draft genome sequence of Brachypodium will be complete by the end of 2007. The list of plant species in the current DOE genome-sequencing pipeline is very short and includes crops that have global economic significance such as sorghum (Sorghum bicolor) and cotton (Gossypium hirsutum). So why has this small weedy wild plant with no intrinsic economic value become a genome-sequencing target for the DOE? Both Brachypodium and domesticated grass crops belong to the plant family Poaceae (Gramineae). The domesticated grass crops encompass an extraordinarily diverse set of species distributed around the world, including the most important crops for human subsistence, i.e. wheat (Triticum aestivum) and rice (Oryza sativa). Other grass crops such as sorghum, maize (Zea mays), barley (Hordeum vulgare), rye (Secale cereale) and oat (Avena sativa) also play important roles in the human food supply.1

“Why has this small weedy plant with no intrinsic economic value become a genome sequencing target?”

Many other perennial grass species are important forage crops for animal feed,2 and still another group of grass species serve an important role as turf grasses. A highly significant area of research that is emerging has identified yet another important and new use of grasses—in this instance as feedstock for conversion to biofuels such as ethanol.3 Thus Brachypodium is a relative to an exceptionally large number of important crops with a broad range of uses. In particular, Brachypodium is more closely related to cool season grass crops that grow in temperate environments than is rice.4 This evolutionary relationship underlies the DOE's interest in Brachypodium.

The promise of biotechnology

Traditional plant breeding has been employed for decades to improve traits that affect crop yield and quality. Nonetheless, crop improvement by traditional breeding alone can encounter a range of barriers that make it challenging to improve some traits. To date, biotechnology has directly or indirectly supplemented traditional plant-breeding programmes in two ways. First, DNA-based marker techniques have provided a mechanism whereby breeders can indirectly select for genes of interest in their germplasm when traditional selection based on phenotype is not efficient. For instance, in wheat, DNA markers linked to genes that confer partial resistance to the fungal disease Fusarium head blight5 have been widely employed. Second, the technique of genetic transformation, in which DNA encoding a useful gene is integrated into a crop genome, has had a profound effect on agriculture, particularly in the USA. This is illustrated by the fact that the majority of the soybean (Glycine max) and cotton now grown in the USA is transformed to contain one or more genes that confer beneficial traits.6

But what will biotechnology contribute to future crop improvement? A deeper understanding of the biological processes associated with factors that can limit crop productivity may provide a road-map that will lead us to devise new strategies for generating better crops through biotechnology in the future. Perhaps the most significant advances will come from the detailed genetic information embedded in the genomes of plants themselves.

Model crops

The nuclear genome sequences of both the dicot model plant Arabidopsis thaliana (Arabidopsis)7 and rice8 have now been deciphered. These sequences have afforded plant scientists an unprecedented look at the gene content and genome organisation of plants and have also provided a wealth of information that can be used to unravel the function of many genes. Recently, a draft genome sequence of Populus trichocarpa, a model system for tree crop improvement and only the third plant genome to be sequenced, was released from the DOE sequencing pipeline.9

Arabidopsis and rice provide contrasting opportunities to identify novel biotechnological approaches to crop improvement. On one hand, Arabidopsis is a true model plant—it is petite and grows rapidly, has a small genome, is self-compatible, exhibits diploid genetics and is easily transformable. Arabidopsis has thus served as a functional genomics system to study a remarkably diverse array of biological processes in plants, and this in turn has led to a plethora of discoveries potentially relevant to crop improvement. Genomics discoveries in Arabidopsis have been exploited in many crops, including distant relatives. For example, the sequence of an Arabidopsis gene involved in gibberellin responsiveness served as the starting point to isolate Rht dwarfing genes in wheat that have contributed to major yield gains in this crop.10

However, as a dicot, Arabidopsis does not share certain features with monocotyledonous plants, which include the domesticated grass crops. Thus, for researchers interested in improving a grass crop, rice would appear to fill this gap. However, while the rice genome sequence is available, the rice plant itself is not a particularly attractive functional genomics model system as is Arabidopsis, partly owing to the fact that rice lacks the petite stature, rapid life cycle and ease of transformation found in Arabidopsis. A further complication is that about 50 million years of evolution separate rice from many important cool season grass crops such as wheat.11 Thus a significant void exists in merging basic plant biology and crop improvement owing to the fact that there is no model system akin to Arabidopsis available for grass crops.

With Brachypodium, this is about to change. Over a decade ago it was recognised that Brachypodium had many innate biological attributes desired in a model plant system,12 and the seminal paper proposing Brachypodium as a model system for cool season grasses was published at the end of 2001.13 The nuclear genome of diploid Brachypodium is very small—about 2.25 times as large as that of Arabidopsis and smaller than that of rice. In fact, the Brachypodium genome is about 2% of the size of the wheat genome, or roughly the size of a single wheat chromosome arm.14 Many diploid ecotypes of Brachypodium are small, and under the appropriate environmental conditions the most rapidly maturing of these can complete its life cycle in 2 months or less,15, 16 which is comparable to Arabidopsis.17 Another highly desirable aspect of Brachypodium is that it is self-pollinating. Thus Brachypodium does indeed possess a plethora of core biological attributes that researchers may desire in a model plant system.

The emergence of Brachypodium

In the last few years the community of scientists becoming involved in Brachypodium research has grown rapidly. This can be attributed to several recent developments. First, a set of inbred diploid Brachypodium lines has been developed and distributed to interested parties.15, 16 This is important, because scientists are now pursuing research with a common set of reference genotypes. Flexible growth conditions that can rapidly induce flowering in the majority of these inbred lines have also been identified, thus permitting rapid generation turnover and relatively easy maintenance of plants.15, 16 Further, transformation of diploid Brachypodium using the widely employed Agrobacterium tumefaciens method has been demonstrated.16 This is significant, because it has become a standard method for functional genomics research. Other important genomics resources are now emerging as well. These include many thousand ESTs,18deep genome coverage large insert bacterial artificial chromosome (BAC) libraries for reference inbred diploid lines,19 and segregating populations from crosses between diploid lines15. Taken as a whole, these resources delineate a core set of tools needed for modern genomics research with Brachypodium. Many more resources are being developed by the scientific community as well and should be available over the course of the next 5 years. These are likely to include mutant pools, microarrays and transposon-tagging systems. Additionally, curation of Brachypodium genomic information will be efficiently managed by appropriate data portals now being established (e.g. Ref. 20).

However, the biggest bang in Brachypodium genomics resources will come in the form of the whole genome sequence from the DOE-supported project. The impetus for the DOE project effort is bipartite. First, the DOE recognised that a structural and functional model plant system for wheat, the historical staff of human civilisation and perhaps still the most important food crop for human subsistence, and other cool season grass crops holds great potential for meeting future food demands. Second, the DOE has a rapidly growing interest in developing biofuels, with grass species such as switchgrass featuring prominently in future plans. A model system for studying how to modify grass crops for increased biofuel production is highly desirable. By virtue of shared evolutionary history, Brachypodium can be used as a model for both goals. The rapid development of core genomics resources for Brachypodium, capped off by the DOE genome-sequencing project, solidifies the position of Brachypodium as the newest model system for crop plant improvement.