6 upon passage through tissue culture [39]. This retrotranspo- son can be used to generate a large population of plants with tagged mutation sites in tissue culture that become stable upon regeneration of whole plants, an important resource for both forward and reverse genetics. A population muta- genized by Tnt1 can be used for reverse genetic screens by sequencing of tagged sites and forward genetic screens by observation of phenotypes. The isolation of the M. truncat- ula pim gene through this reverse genetics approach demon- strates the utility of the system for identifying mutants by se- quence [40]. 6. TRANSLATIONAL GENOMICS FROM MODEL TO CROP LEGUMES The value of the model systems will be enhanced by the abil- ity to connect model systems to crops at the structural and functional genome levels. For example, conserved genome structure (synteny) between model and crop species could al- low the use of model species as a surrogate genome for map- based cloning of agronomically important genes in crops with complex genomes. Moreover, detailed knowledge of the molecular basis of conserved phenotypes in model species can be translated to great advantage for gene discovery in related species. Working with M. truncatula as a reference system, researchers have used comparative genomics tools to bridge model and crop legumes through comparative mapping of orthologous genes [54, 124, 125]. Alignment of linkage maps and sequenced orthologous regions reveals an extensive network of macro- and microsynteny between legume species [125–127]. In fact, the conserved genome or- ganization between M. truncatula and crop legumes has al- lowed for cross-species prediction and isolation of several genes required for root symbiosis using M. truncatula as a surrogate [128, 129] and reviewed in [125]. Despite the emerging picture of substantial synteny between legumes, the level of conservation decreases as the evolutionary dis- tance increases [124, 125]. Thus, comparisons within Gale- goid or Phaseolid legumes tend to reveal chromosome-level synteny, while comparisons between the two clades tend to reveal large-segment synteny, which is also reﬂected in the diﬀerences in chromosome number between Galegoid and Phaseolid legumes [125, 127].The broad taxonomic distance separating the two clades warrants the development of one or two reference systems within each clade, M. truncatula, and L. japonicus for the cool-season legumes and soybean for the tropical-season legumes [130]. A signiﬁcant eﬀort has been undertaken in compara- tive genomic analysis of legume resistance gene homologs (RGHs). Most plant disease resistance genes identiﬁed to date belong to the nucleotide binding site (NBS) leucine rich re- peat (LRR) family [131]. NBS-LRR genes can be further clas- siﬁed by the presence or absence of a toll/interleukin recep- tor (TIR) homology domain. In previous studies, researchers investigated the genomic architecture of RGHs in M. trun- catula [21], and used phylogenetic methods to assess evolu- tionary trends in this large gene family in legumes and across the angiosperms [21, 132]. The results from these studies revealed several important insights into RGH gene evolu- International Journal of Plant Genomics tion in plants. Despite the presence of the two major lin- eages of RGHs (i.e., TIR and non-TIR NBS-LRR genes) in all dicots, each of these lineages is populated by numerous family-speciﬁc or family-predominant clades [132]. For ex- ample, the major RGH clades that deﬁne legumes are absent from the Brassicaceae and Solanaceae, and vice versa. Thus, there are likely to be aspects of RGHs (including both struc- tural and functional attributes) that are peculiar to individual plant families. When phylogenetic analyses were conducted within the legume family [21], it was found that all known major clades in legumes are represented by sequences from M. truncatula, providing evidence that the major RGH radi- ations predate the respective speciation events. There are also cases that cophyletic RGHs occupy syntenic positions be- tween legumes. The availability of a nearly complete catalog of M. truncatula NBS-LRR genes is expected to greatly enable rapid and eﬃcient characterization of RGHs in other closely related legumes. A legume genome project towards this ef- fort has recently been funded by the NSF Plant Genome Re- search Program. The goal of this funded project was to de- velop genomic tools for ﬁve less-studied legume species (i.e., chickpea, pigeon pea, cowpea, peanut, and lupine), which are economically important in the developing countries of Africa and Asia (D. R. Cook, personal communication). Forage legumes, such as alfalfa, red clover, and white clover, are an important component of animal and sustain- able agriculture throughout the world. In addition to pro- viding superior forage quality for animal production and improving soil fertility through nitrogen ﬁxation, forage legumes also contribute to the improvement of soil struc- ture and control of soil erosion. Alfalfa (Medicago sativa), for example, is grown on over 26 million acres and ranks third in acreage planted and dollar value in the US (USDA Crop Values Summary 2005). The true clovers (Trifolium spp.), which are often grown together with forage grasses, are also widely distributed. Despite serving as a major source of meat and milk products via animals, the economic im- portance of forages to food production and the agricultural economy of the US are not fully appreciated. Consequently, forage legumes suﬀer from poorly developed genetic and ge- nomic infrastructure due to both limited federal funding and their intractable genetic system (e.g., polyploidy and self-incompatibility). The lack of such infrastructure limits the application of genomics-enabled technologies in the ge- netic improvement of forage legumes. Nevertheless, all these forage legumes are closely related to the model legume M. truncatula, a cool-season legume within the tribe Trifolieae. Therefore, forage legumes could be an immediate beneﬁ- ciary of the study of M. truncatula genomics. As many of the pathogens of M. truncatula are also pathogens of closely re- lated forage legumes, it should be possible to clone resistance genes that are active against pathogens of crop legume species in M. truncatula. In addition, due to the close relationship of resistance gene sequences between these species, it is likely that functional resistance genes can be moved across species boundaries by transgenic approaches. Thus the genetic, genomic, and molecular tools avail- able in M. truncatula allow not only investigation of basic