The Samuel Roberts Noble Foundation, Inc.

Center for Medicago Genomics Research

The Fabaceae (legumes) are second only to the Poaceae (grasses) in importance to humans as a source of food, feed for livestock, and raw materials for industry (Graham and Vance, 2003). Seeds and shoots of legumes are a rich source of dietary protein, oil, carbohydrates, fiber, minerals, vitamins, and other beneficial secondary compounds for humans and livestock (Wang et al., 2003). Legumes account for approximately one third of the world's primary crop production, human dietary protein, and processed vegetable oil. Food legumes of global importance include common bean, soybean, pea, chickpea, broad bean, pigeon pea, cowpea and lentil. Important forage legumes include alfalfa, white and red clover, and various Lotus species. Apart from their use as food and feed, legumes are used in soil conservation, phytoremediation, lumber production, as ornamental herbs and bushes, and for extraction of gums, resins or food additives.

Legumes are a lynch pin of sustainable agriculture because they supply their own nitrogen (N) by 'fixing' it in a symbiotic association with bacteria called rhizobia. This mutually beneficial association provides legumes and subsequent crops with a free and renewable source of usable nitrogen. It is estimated that between 40 million and 60 million tonnes of nitrogen are fixed annually by cultivated legumes (Smil, 1999), equivalent to about US$10 billion fertilizer (Graham and Vance, 2003). Legumes also form mutualistic symbioses with mycorrhizal fungi that provide their host plant with phosphorous and other soil nutrients, which enhance plant growth. On the other hand, legumes suffer from numerous pests and pathogens, which negatively effect plant growth and agricultural yield.

The complex interactions of legumes with microorganisms have resulted in the evolution of a rich variety of natural product biosynthetic pathways impacting both mutualistic and disease/defense interactions. For example, legume isoflavonoids induce expression of genes in rhizobia that are required for nodulation and symbiotic nitrogen fixation, and pterocarpan phytoalexins are involved in host disease resistance. Different secondary compounds have anticancer and other health promoting effects in humans (Dixon and Sumner, 2003; Dixon, 2004). The phenylpropanoid polymer lignin is ubiquitous in monocots and dicots, and is important in forage legumes such as alfalfa because of its negative impact on forage digestibility.

Scientists at the Noble Foundation carry out fundamental and applied research on legumes to better understand the molecular basis of beneficial and detrimental plant-microbe interactions, plant responses to abiotic stresses such as drought, soil acidity and aluminum toxicity, and how primary and secondary metabolism is organized and regulated to produce compounds of value to humans, livestock, and industry. Through a better understanding of these processes and the genes involved, we hope to optimize symbioses, enhance legume tolerance of abiotic and biotic stresses, and fine-tune metabolism to produce more nutritious and health-promoting compounds through molecular breeding strategies in the future. In fact, the future is near for some of these objectives, such as the production of low-lignin alfalfa with improved digestibility and nutritive value for animals.

While pasture and crop legumes are the ultimate targets of applied research at the Noble Foundation, most of these species are poor model systems for experimental research. Some cultivated legumes are tetraploid (e.g. alfalfa and peanut), many have large genomes (e.g. pea and Faba beans) and many are recalcitrant to transformation or difficult to regenerate (e.g. common bean, pea and soybean). Most grain legumes have large seeds, relatively few seeds per plant, and large seedlings, which prevents high-density culture (e.g. chickpea, Vigna, pea, beans and soybean). Some legumes, such as soybean, have genome duplications and some are self-incompatible or have a long generation time. As a result, two other species, Medicago truncatula and Lotus japonicus, have been adopted internationally as models for legume research (Barker et al., 1990; Handberg and Stougaard, 1992).

Medicago truncatula (commonly called barrel medic or simply Medicago) is the primary model, or reference legume species for genomic and functional genomic research in the USA (Barker et al., 1990; Cook, 1999). Medicago has a number of features that make it an excellent model for other legume species. First, as a member of the Papilionoideae sub-family of the legumes, Medicago is closely related to the majority of crop and pasture legumes, its nearest cousin in this respect being alfalfa (Medicago sativa), the most important forage legume in the USA (Choi et al., 2004b). Second, Medicago has a relatively small, diploid genome (haploid size approx. 550 Mbp), making it useful for both genetics and genomics (Young et al., 2005). Third, it is self-fertile and produces a large number of seed on a plant of relatively small stature, making it amenable to high-density culture (Barker et al., 1990). Finally, it is relatively easy to transform, which makes it suitable for reverse genetics experiments (Chabaud et al., 2003; Araújo et al., 2004; Crane et al., 2006). Since its adoption by the international community as a model species, a number of useful tools and resources have been developed for Medicago, including high-density genetic and physical maps for genetics research (Thoquet et al., 2002; Choi et al., 2004a), a variety of different kinds of mutant populations, including EMS, fast-neutron deletion, and transposon insertion mutants (Tadege et al., 2005), and tools and protocols for transcriptome, proteome, and metabolome analysis (Gallardo et al., 2003; Watson et al., 2003; Barnett et al., 2004; Manthey et al., 2004; Broeckling et al., 2005; Benedito et al., 2008). The most recent addition to the functional genomics toolkit for Medicago is the creation of the Medicago Gene Expression Atlas, which provides quantitative gene expression data for the majority of Medicago genes during plant development and in response to environmental stimuli (Benedito et al., 2008). Noble Foundation scientists have played a leading role in establishing many of these resources, through both internal and external funding.

Noble Medicago Genomics Research
Noble Medicago Genomics Research
Noble Medicago Genomics Research
Noble Medicago Genomics Research
 

An important sign that Medicago had come of age as a research model was the commencement of genome sequencing of this species. In 2001, the Noble Foundation invested $5 million to initiate this effort (Bell et al., 2001) and subsequent international funding by the governments of the USA (NSF) and the European Union will take the project through completion of at least of the gene-rich regions of the genome (Young et al., 2005). Investments in Medicago genetic and genomic resources have paid off handsomely in the past few years, especially in the area of symbiotic nitrogen fixation (SNF) research, where a number of genes involved in nodule development have been cloned for the first time (reviewed in (Oldroyd and Downie, 2004; Udvardi and Scheible, 2005)). These novel tools and resources are being applied to several research areas at the Noble Foundation, including seed development and storage metabolism; organization, regulation, and structural biology of secondary metabolism; bioinformatics and comparative genomics; symbiotic nitrogen fixation; improvement of drought tolerance and phosphorus uptake, and plant-pathogen interactions, including cotton root rot disease, one of the most destructive diseases of cotton and alfalfa (Medicago sativa) in the South West United States.

Knowledge gained from genomics and functional genomics research on Medicago truncatula is being utilized to improve important forage and grain legumes. In fact, this process of translational genomics from model to crop species, especially cool-season forage legumes is one of the flagship enterprises that link numerous groups within all three divisions of the Noble Foundation.

Last updated: 10/05/09