The Switchgrass Genome: Tools and Strategies

Switchgrass (Panicum virgatum L.) is a perennial grass species receiving signifi cant focus as a potential bioenergy crop. In the last 5 yr the switchgrass research community has produced a genetic linkage map, an expressed sequence tag (EST) database, a set of single nucleotide polymorphism (SNP) markers that are distributed across the 18 linkage groups, 4x sampling of the P. virgatum AP13 genome in 400-bp reads, and bacterial artifi cial chromosome (BAC) libraries containing over 200,000 clones. These studies have revealed close collinearity of the switchgrass genome with those of sorghum [Sorghum bicolor (L.) Moench], rice (Oryza sativa L.), and Brachypodium distachyon (L.) P. Beauv. Switchgrass researchers have also developed several microarray technologies for gene expression studies. Switchgrass genomic resources will accelerate the ability of plant breeders to enhance productivity, pest resistance, and nutritional quality. Because switchgrass is a relative newcomer to the genomics world, many secrets of the switchgrass genome have yet to be revealed. To continue to effi ciently explore basic and applied topics in switchgrass, it will be critical to capture and exploit the knowledge of plant geneticists and breeders on the next logical steps in the development and utilization of genomic resources for this species. To this end, the community has established a switchgrass genomics executive committee and work group (http://switchgrassgenomics.org/ [verifi ed 28 Oct. 2011]). BACKGROUND SWITCHGRASS (Panicum virgatum L.) is a perennial C4 grass native to North America that is broadly adapted for growth across much of North and Central America. It has been the focus of agronomic, breeding, and genetics research since the 1950s, largely focused on development of cultivars and management systems for livestock production in the Great Plains region of the United States (Vogel, 2004). Research on switchgrass was intensifi ed in 1992 when the U.S. Department of Energy (USDOE) chose Published in The Plant Genome 4:273–282. Published 7 Dec. 2011. doi: 10.3835/plantgenome2011.10.0026 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. M.D. Casler, USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI 53706-1108; C.M. Tobias, USDA-ARS, Western Regional Research Center, Albany, CA 94710; S.M. Kaeppler, Dep. of Agronomy, Univ. of Wisconsin, 1575 Linden Dr., Madison, WI 53706; C.R. Buell, Dep. of Plant Biology, Michigan State Univ., East Lansing, MI 48824-1312; Z. Wang, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK 73401; P. Cao, Dep. Plant Pathology, Univ. of California, Davis, and the UC-Davis Genome Center, CA, and China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China 450001; J. Schmutz, HudsonAlpha Institute of Biotechnology, Huntsville, AL, and Dep. of Energy Joint Genome Institute, Walnut Creek, CA; P. Ronald, The Joint Bioenergy Institute, Emeryville, Dep. Plant Pathology, Univ. of California-Davis, and the UC-Davis Genome Center, Davis, CA 95616. Received 10 Oct. 2011. *Corresponding author ([email protected]). Abbreviations: ARS, Agricultural Research Service; BAC, bacterial artifi cial chromosome; BES, bacterial artifi cial chromosome end sequence; BESC, Bioenergy Sciences Center; BFDP, Biofuels Feedstock Development Program; COMT, caffeic acid O-methyltransferase; EST, expressed sequence tag; FES, fosmid end sequence; GC, guanine–cytosine; GE, genetically engineered; GLBRC, Great Lakes Bioenergy Research Center; GRIN, Germplasm Resources Information Network; JBEI, USDOE Joint Bioenergy Institute; JGI, Joint Genome Institute; NGS, next-generation genetics; NPGS, National Plant Germplasm System; NRCS, Natural Resource Conservation Service; RFLP, restriction fragment length polymorphism; SGEC, Switchgrass Genetics Executive Committee; SNP, single nucleotide polymorphism; SRNF, Samuel Roberts Noble Foundation; SSR, simple sequence repeat; STS, sequence tagged site.