Journal of the Science of Food and Agriculture J Sci Food Agric 87:1177–1179 (2007)

Spotlight Brachypodium: a new monocot model plant system emerges

sequence tags (ESTs) from the same species (http://www.jgi.doe.gov/sequencing/why/CSP2007/ brachypodium.html). 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 cur- rent DOE genome-sequencing pipeline is very short and includes crops that have global economic signif- icance 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 Brachy- podium 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)andrice(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 Shoulder to shoulder: Brachypodium (right) may prove as useful as Arabidopsis (left). value become a genome

The small grass species Brachypodium distachyon sequencing target?’’ (purple false brome) is potentially an ideal model plant system for grass crop research. To realise this Many other perennial grass species are important potential, a range of genetic and genomic resources forage crops for animal feed,2 and still another group have been developed in a very short period of time, of grass species serve an important role as turf grasses. and more still are in the pipeline. David Garvin A highly significant area of research that is emerging explains how these resources will establish has identified yet another important and new use of B. distachyon as the newest model plant system grasses – in this instance as feedstock for conversion and will fill a long-empty void in genomics resources to biofuels such as ethanol.3 Thus Brachypodium is a for grass crop improvement. 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 Working grass hero grass crops that grow in temperate environments than Early in 2006 the US Department of Energy is rice.4 This evolutionary relationship underlies the (DOE) approved a project to sequence the DOE’s interest in Brachypodium. nuclear genome of the wild grass species Brachy- podium distachyon (Brachypodium); this project The promise of biotechnology was coupled with an accompanying project to Traditional plant breeding has been employed for sequence nearly a quarter of a million expressed decades to improve traits that affect crop yield and

Keywords: genome sequencing; monocots; model systems; grass; Brachypodium distachyon (Received 3 November 2006; revised version received 12 December 2006; accepted 18 December 2006) Published online 11 April 2007; DOI: 10.1002/jsfa.2868

This article is a US Government work and is in the public domain in the USA. J Sci Food Agric 0022–5142/2007/$30.00 DF Garvin quality. Nonetheless, crop improvement by traditional include the domesticated grass crops. Thus, for breeding alone can encounter a range of barriers that researchers interested in improving a grass crop, rice make it challenging to improve some traits. To date, would appear to fill this gap. However, while the biotechnology has directly or indirectly supplemented rice genome sequence is available, the rice plant itself traditional plant-breeding programmes in two ways. is not a particularly attractive functional genomics First, DNA-based marker techniques have provided a model system as is Arabidopsis, partly owing to the mechanism whereby breeders can indirectly select for fact that rice lacks the petite stature, rapid life cycle genes of interest in their germplasm when traditional and ease of transformation found in Arabidopsis. A selection based on phenotype is not efficient. For further complication is that about 50 million years instance, in wheat, DNA markers linked to genes of evolution separate rice from many important cool that confer partial resistance to the fungal disease season grass crops such as wheat.11 Thus a significant Fusarium head blight5 have been widely employed. void exists in merging basic plant biology and crop Second, the technique of genetic transformation, in improvement owing to the fact that there is no model which DNA encoding a useful gene is integrated into a system akin to Arabidopsis available for grass crops. crop genome, has had a profound effect on agriculture, With Brachypodium, this is about to change. Over particularly in the USA. This is illustrated by the a decade ago it was recognised that Brachypodium fact that the majority of the soybean (Glycine max) had many innate biological attributes desired in andcottonnowgrownintheUSAistransformed a model plant system,12 and the seminal paper to contain one or more genes that confer beneficial proposing Brachypodium as a model system for cool traits.6 season grasses was published at the end of 2001.13 But what will biotechnology contribute to future The nuclear genome of diploid Brachypodium is crop improvement? A deeper understanding of the very small – about 2.25 times as large as that of biological processes associated with factors that can Arabidopsis and smaller than that of rice. In fact, limit crop productivity may provide a road-map that the Brachypodium genome is about 2% of the size will lead us to devise new strategies for generating of the wheat genome, or roughly the size of a single better crops through biotechnology in the future. wheat chromosome arm.14 Many diploid ecotypes of Perhaps the most significant advances will come from Brachypodium are small, and under the appropriate the detailed genetic information embedded in the environmental conditions the most rapidly maturing of genomes of plants themselves. these can complete its life cycle in 2 months or less,15,16 which is comparable to Arabidopsis.17 Another highly Model crops desirable aspect of Brachypodium is that it is self- The nuclear genome sequences of both the dicot pollinating. Thus Brachypodium does indeed possess model plant Arabidopsis thaliana (Arabidopsis)7 and 8 a plethora of core biological attributes that researchers rice have now been deciphered. These sequences have may desire in a model plant system. afforded plant scientists an unprecedented look at the gene content and genome organisation of plants and The emergence of Brachypodium have also provided a wealth of information that can be In the last few years the community of scientists used to unravel the function of many genes. Recently, a becoming involved in Brachypodium research has draft genome sequence of Populus trichocarpa,amodel grown rapidly. This can be attributed to several recent system for tree crop improvement and only the third developments. First, a set of inbred diploid Brachy- plant genome to be sequenced, was released from the podium lines has been developed and distributed to DOE sequencing pipeline.9 interested parties.15,16 This is important, because sci- Arabidopsis and rice provide contrasting opportu- entists are now pursuing research with a common nities to identify novel biotechnological approaches set of reference genotypes. Flexible growth condi- to crop improvement. On one hand, Arabidopsis is a tions that can rapidly induce flowering in the majority true model plant – it is petite and grows rapidly, has of these inbred lines have also been identified, thus a small genome, is self-compatible, exhibits diploid permitting rapid generation turnover and relatively genetics and is easily transformable. Arabidopsis has easy maintenance of plants.15,16 Further, transfor- thus served as a functional genomics system to study mation of diploid Brachypodium using the widely a remarkably diverse array of biological processes employed Agrobacterium tumefaciens method has been in plants, and this in turn has led to a plethora demonstrated.16 This is significant, because it has of discoveries potentially relevant to crop improve- become a standard method for functional genomics ment. Genomics discoveries in Arabidopsis have been research. Other important genomics resources are exploited in many crops, including distant relatives. now emerging as well. These include many thousand For example, the sequence of an Arabidopsis gene ESTs,18deep genome coverage large insert bacterial involved in gibberellin responsiveness served as the artificial chromosome (BAC) libraries for reference starting point to isolate Rht dwarfing genes in wheat inbred diploid lines,19 and segregating populations that have contributed to major yield gains in this from crosses between diploid lines15. Taken as a crop.10 whole, these resources delineate a core set of tools However, as a dicot, Arabidopsis does not share needed for modern genomics research with Brachy- certain features with monocotyledonous plants, which podium. Many more resources are being developed

1178 J Sci Food Agric 87:1177–1179 (2007) DOI: 10.1002/jsfa Brachypodium: a new monocot model plant system by the scientific community as well and should be 4 Kellogg EA, Evolutionary history of the grasses. Plant Physiol available over the course of the next 5 years. These 125:1198–1205 (2001). 5 Liu S and Anderson JA, Marker assisted evaluation of Fusarium head are likely to include mutant pools, microarrays and blight resistant wheat germplasm. Crop Sci 43:760–766 (2003). transposon-tagging systems. Additionally, curation of 6 Fernandez-Cornejo J and McBride WD, Adoption of bioengineered Brachypodium genomic information will be efficiently crops. USDA-ERS Rep. 810 (2002). managed by appropriate data portals now being estab- 7 The Arabidopsis Initiative, Analysis of the genome sequence of the lished (e.g. Ref. 20). flowering plant Arabidopsis thaliana. Nature 408:796–815 (2000). 8 International Rice Genome Sequencing Project, The map-based sequence However, the biggest bang in Brachypodium of the rice genome. Nature 436:793–800 (2005). genomics resources will come in the form of the whole 9 Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, genome sequence from the DOE-supported project. et al., The genome of black cottonwood, Populus trichocarpa (Torr. & The impetus for the DOE project effort is bipartite. Gray). Science 313:1596–1604 (2006). First, the DOE recognised that a structural and 10 Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, et al., ‘Green revolution’ genes encode mutant gibberellin response functional model plant system for wheat, the historical modulators. Nature 400:256–261 (1999). staff of human civilisation and perhaps still the most 11 Gaut B, Evolutionary dynamics of grass genomes. New Phytol 154:15–28 important food crop for human subsistence, and other (2002). cool season grass crops holds great potential for 12 Bablak P, Draper J, Davey MR and Lynch PT, Plant regeneration and meeting future food demands. Second, the DOE has micropropagation of Brachypodium distachyon. Plant Cell Tissue Organ Cult 42:97–107 (1995). a rapidly growing interest in developing biofuels, with 13 Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, grass species such as switchgrass featuring prominently et al., Brachypodium distachyon. A new model system for functional in future plans. A model system for studying how to genomics in grasses. Plant Physiol 127:1539–1555 (2001). modify grass crops for increased biofuel production 14 Bennett MD and Leitch IJ, Nuclear DNA amounts in angiosperms: is highly desirable. By virtue of shared evolutionary progress, problems, and prospects. Ann Bot 95:45–90 (2005). 15 Garvin DF, Brachypodium distachyon – a new model plant for structural history, Brachypodium can be used as a model for and functional analysis of grass genomes, in Model Plants and Crop both goals. The rapid development of core genomics Improvement, ed. by Koebner RMD and Varshney RK. CRC Press, resources for Brachypodium, capped off by the DOE Boca Raton, FL, pp. 109–123 (2006). genome-sequencing project, solidifies the position of 16 Vogel JP, Garvin DF, Leong OM and Hayden DM, Agrobacterium- Brachypodium as the newest model system for crop mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell Tissue Organ Cult 85:199–211 plant improvement. (2006). 17 Boyes DC, Zayed AM, Ascenzi R, McCaskill AJ, Hoffman NE, David – David F Garvin is at USDA-ARS Plant Science KR, et al., Growth stage-based phenotypic analysis of Arabidopsis: a Research Unit and Department of Agronomy and Plant model for high throughput functional genomics in plants. Plant Cell 13:1499–1510 (2001). Genetics, University of Minnesota, 411 Borlaug Hall, 18 Vogel JP, Gu YQ, Twigg P, Lazo GR, Laudencia-Chingcuanco D, 1991 Upper Buford Circle, St Paul, MN 55108, USA. Hayden DM, et al., EST sequencing and phylogenetic analysis of the [email protected] model grass Brachypodium distachyon. Theor Appl Genet 113:186–195 (2006). 19 Huo N, Gu YQ, Lazo GR, Vogel J, Coleman-Derr D, Luo M-C, et al., References Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 1OlsonRAandFreyKJ,Nutritional Quality of Cereal Grains: Genetic and 49:1099–1108 (2006). Agronomic Improvement. ASA, Madison, WI (1987). 20 [Online]. Available: http://www.brachypodium.org/ [18 December 2006]. 2 Moser LE, Buxton DR and Casler MD, Cool-season Forage Grasses.ASA, Madison, WI (1996). 3 US DOE, Breaking the biological barriers to cellulosic ethanol: a joint research agenda. DOE/SC-0095, US Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy (2006).

J Sci Food Agric 87:1177–1179 (2007) 1179 DOI: 10.1002/jsfa