Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2008, Article ID 256597, 11 pages doi:10.1155/2008/256597 Review Article Recent Advances in Medicago truncatula Genomics Jean-Michel An e´,1 Hongyan Zhu,2 and Julia Frugoli3 1 Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA 2 Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA 3 Department of Genetics and Biochemistry, Clemson University, 100 Jordan Hall, Clemson, SC 29634, USA Correspondence should be addressed to Julia Frugoli, jfrugol@clemson.edu Received 2 April 2007; Accepted 14 September 2007 Recommended by Yunbi Xu Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodu- lation, these two models are now widely used in a variety of biological ﬁelds from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed. Copyright © 2008 Jean-Michel Ane´ et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1. INTRODUCTION Legumes are usually deﬁned by their typical ﬂower structure and the ability of many of them to form root nodules in pres- ence of symbiotic bacteria named rhizobia. With more than 18 000 species, legumes are found from the artic circle to the tropics and include many crops of agronomic importance for grain production, pasture, and forestry [1, 2]. The ability of more than 88% of legumes to obtain nitrogen from the air through root nodules was probably a major determinant in this evolutionary, ecological, and economical success [3]. In- terestingly, the study of symbiotic associations with rhizobia as well as with arbuscular mycorrhizal (AM) fungi also drove the development of two model legumes: Medicago truncatula Gaertner and Lotus japonicus (Regel) K. Larsen. While M. truncatula is an annual medic from the Tri- folieae tribe and a close relative of alfalfa and clovers, L. japonicus belongs to the Loteae and is more distant from cul- tivated cool season legumes than M. truncatula. This phy- logenetic distance to economically important crops is criti- cal in the choice of M. truncatula by many researchers and support by numerous funding agencies. The use of both model legumes allows unique comparative genomic stud- ies within the legume family as well as the comparison be- tween two patterns of root nodule development: indetermi- nate with a persistent nodule meristem in the case of M. trun- catula and determinate in L. japonicus. Unfortunately, these two models belong to the same cool season legumes (Gale- goid clade), whereas soybean and common bean are tropical season legumes (Phaseolid clade). Soybean is therefore pro- posed as a third model legume for both its own economic weight and the phylogenetic proximity to other important crops [4, 5]. Research eﬀorts on model legumes and especially on M. truncatula encompass a broad range of ﬁelds in plant biol- ogy from population biology [6–8] and plant development [9–16] to plant pathology [17–22], insect resistance [23– 27], and biotechnology production [28]. The goal of this review is to provide an overview of the natural characteris- tics and genetic and genomic tools that make M. truncatula such a desirable experimental system for a growing number of plant biologists. We will highlight how information gained from M. truncatula can be transferred to other legumes crops through comparative genomics and we will share our vi- sion of how M. truncatula can allow us to reach the goal of sustainable well-being through sustainable food and biofuel production.