The Plant Genome [A Supplement to Crop Science] ■ March 2008 ■ No. 1 S-69 Development of Genetic and Genomic Research Resources for Brachypodium distachyon , a New Model System for Grass Crop Research David F. Garvin,* Yong-Qiang Gu, Robert Hasterok, Samuel P. Hazen, Glyn Jenkins, Todd C. Mockler, Luis A. J. Mur, and John P. Vogel 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 fills an important gap in grass crop genomics research. A surge in interest in Brachypodium has led to rapid and significant 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 fide model plant system. Before 2001, the unassuming grass genus Brachypo- dium was perhaps more known for its enigmatic fea- tures 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 fam- ily 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, Brachypo- dium possesses the suite of traits desired in a model D.F. Garvin, USDA-ARS Plant Science Research Unit and Dep. of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Cir., St. Paul, MN 55108; Y.-Q. Gu and J.P. Vogel, Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710; R. Hasterok, Dep. of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, 40-032 Katowice, Poland; S.P. Hazen, Dep. of Biochemistry, The Scripps Research Institute, La Jolla, CA 92037; G. Jenkins and L.A.J. Mur, Institute of Biological Sciences, University of Wales, Aberystwyth, Penglais, Aberystwyth, Ceredigion, SY23 3DA, UK; T.C. Mockler, Center for Genome Research and Biocomputing, Dep. of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331. Research supported by Polish Ministry of Science and Higher Education Grant 2 PO4C 012 30 to R. Hasterok, and by Ruth L. Kirschstein National Research Service Award postdoctoral fellowship GM071225 to S.P. Hazen. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. Received 12 June 2007. *Corresponding author (garvi007@umn.edu). Published in Crop Sci. 48(S1) S69–S84. Published 8 Feb. 2008. doi:10.2135/cropsci2007.06.0332tpg © Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Abbreviations: BAC, bacterial artificial chromosome; BES, BAC end sequence; cDNA, complimentary DNA; DNA, deoxyribonucleic acid; DOE, Department of Energy; EST, expressed sequence tag; FISH, fluorescent in situ hybridization; GUS, β - glucoronidase; HR, hypersensitive response; JGI, Joint Genome Initiative; kb, kilobase pair; NPGS, National Plant Germplasm System; ORF, open reading frame; PCR, polymerase chain reaction; QR, qualitative resistance; QTL, quantitative trait locus; RNAi, ribonucleic acid interference; SAR, systemic acquired resistance; SNP, single nucleotide polymorphism; T-DNA, transfer-DNA. Ge ome The Ge ome The Activities & Resources