Update on Comparative Genomics of Legumes Bridging Model and Crop Legumes through Comparative Genomics

The Fabaceae, or legumes, constitute the third largest family of flowering plants, comprising more than 650 genera and 18,000 species (Polhill and Raven, 1981). Economically, legumes represent the second most important family of crop plants after Poaceae (grass family), accounting for approximately 27% of the world’s crop production (Graham and Vance, 2003). On a worldwide basis, legumes contribute about onethird of humankind’s protein intake, while also serving as an important source of fodder and forage for animals and of edible and industrial oils. One of the most important attributes of legumes is their unique capacity for symbiotic nitrogen fixation, underlying their importance as a source of nitrogen in both natural and agricultural ecosystems. Legumes also accumulate natural products (secondary metabolites) such as isoflavonoids that are beneficial to human health through anticancer and other health-promoting activities (Dixon and Sumner, 2003). The legumes are highly diverse and can be divided into three subfamilies: Mimosoideae, Caesalpinioideae, and Papilionoideae (Doyle and Luckow, 2003). Of these, the Papilionoideae subfamily contains nearly all economically important crop legumes, including soybean (Glycine max), peanut (Arachis hypogaea), mungbean (Vigna radiata), chickpea (Cicer arietinum), lentil (Lens culinaris), common bean (Phaseolus vulgaris), pea (Pisum sativum), and alfalfa (Medicago sativa). With the notable exception of peanut, all these important crop legumes fall into two Papilionoid clades, namely, Galegoid andPhaseoloid,which are often referred to as cool season and tropical season legumes, respectively (Fig. 1). Despite their close phylogenetic relationships, crop legumes differ greatly in their genome size, base chromosome number, ploidy level, and selfcompatibility (Table I). Nevertheless, earlier studies indicated that members of the Papilionoideae subfamily exhibited extensive genome conservation based on comparative genetic mapping (Weeden et al., 1992; Menancio-Hautea et al., 1993). To establish a unified genetic system for legumes, two legume species in the Galegoid clade,Medicago truncatula and Lotus japonicus, which belong to the tribes Trifolieae and Loteae, respectively,were selected asmodel systems for studying legume genomics and biology (Cook, 1999; Stougaard, 2001). Unlike many of the major crop legumes, M. truncatula and L. japonicus are of small genome size, amenable to forward and reverse genetic analyses, and well suited for studying biological issues important to the related crop legume species. An immediate goal of legume genomics is to transfer knowledge betweenmodel and crop legumes. Accordingly, an in-depth understanding of conservation of genome structure among legume species is a prerequisite to achieving this goal. The idea that conserved genome structure can facilitate transfer of knowledge among relatedplant species is best addressed ingrasses in which genome macrosynteny and microsynteny have been extensively maintained (Bennetzen, 2000; Devos and Gale, 2000). These studies, however, also revealedmany exceptions to the conserved synteny, with frequent local genic rearrangements including gene inversion, duplication, translocation, and insertion/ deletion. Although the degeneracy of local genome microstructure has been widely documented, it is less clear the extent to which such alterations to genome microstructure contribute to the divergence of genome function. In this review, we focus on recent results of comparative genome analysis betweenmodel and crop legumes, and also highlight the recent successes of using comparative genomics tools for cross-species gene isolation.