03 October 2012

Notes on a model species

2012.09.20 - Seeds Seeds. Photo by jby.
There are a couple of neat racks on my desk containing rows of plastic tubes, each tube with a drift of tiny, kidney-bean-shaped seeds at the bottom. These are seeds of Medicago truncatula, barrel medick. When I tell people about this plant I'm currently studying, I usually describe it as an unremarkable wildflower native to the Mediterranean. Or I note that it's a close-ish relative of alfalfa (Medicago sativa).

Medicago truncatula does not have an especially grand heritage. It grows in dry, sunny places throughout the dry, sunny Mediterranean region, forming low tangles of trifoliate leaves and small yellow flowers that eventually ripen into tough, spiky, vaguely barrel-shaped fruits full of those tiny seeds. Some of the seeds on my desk are descended from plants that grew in places like the Temple of Apollo at Curium, Cyprus; but most are from less distinguished locales. In his 2011 monograph on the genus Medicago, Ernest Small quotes a description of M. truncatula's habitat as "sandy fields, wet grasslands, wet meadows, strongly overgrazed and degraded garrique, coniferous forests, grasslands, fallow fields, olive groves, and as a weed in cereal and crops and waste places."

Although the genus Medicago is moderately diverse and widespread across Europe, M. truncatula didn't make it into Carolus Linnaeus's classification as a separate species. Digging into the depths of JSTOR, I can find truncatula in the inventory of seeds archived at the Royal Botanic Gardens at Kew for 1889, but listed under the name M. tribuloides, which has since been deprecated.

2012.08.29 - Germination Germinating. Photo by jby.
Charles Darwin used black medick, Medicago lupulina, in one of his many experiments in self-pollination—he found that plants cut off from visiting bees by netting produced fewer seeds that those left open. But the earliest mention of an experiment with M. truncatula that I can find is a 1966 study of germination conditions in "range plants" by a couple of Israeli scientists who were, presumably, looking for candidates to help make the desert bloom. Meanwhile, in Australia, ranchers found that M. truncatula made a useful drought-tolerant forage plant. Barrel medick first landed Down Under some time before the 1920s; now, more than 4.5 million hectares are sewn with M. truncatula—almost a fifth of the area of the state of Minnesota.

References to Medicago truncatula genetic studies, and the plant's use in experiments on the nitrogen fixation mutualism with rhizobial bacteria—both its general function and its basic biochemistry—begin to show up in the 1960s and 70s. Most of this research, conducted by Australian biologists and agronomists, focused on improving the plant's use for forage.

Barrel medick makes a pretty friendly experimental subject: individual plants don't take up too much space or need too much care, and they grow from seed to fruiting in only three or four months. Moreover, unlike black medick, barrel medick is quite self-fertile—so that after enough inbreeding, a barrel medick plant left on its own will produce seeds that are genetically identical to their parent. That allows experiments with multiple replicates of each genetic line, which can measure genetic effects with high precision. Artificially mutated lines and genetic markers could further help to track down genes important in development and the nitrogen fixation mutualism. Researchers in Australia, the United States, and France started research collections of seeds from naturally varying lines of the plant. People started calling Medicago truncatula a model legume.

2012.09.02 - Sprout Sprouting. Photo by jby.
The body of research work with Medicago truncatula, the practical value of understanding the genetics underlying nitrogen fixation, and the fact that the plant has a relatively small, diploid genome (about 500 million base pairs, if you're counting), helped make the case for building a whole-genome sequence, which was undertaken by an international collaboration of American and French biologists. The team announced a publication-worthy draft genome in Nature just at the end of 2011. The actual genome sequenced belongs to a line of Medicago truncatula developed as a livestock forage cultivar in Australia, which is named after the biological research station where it was first collected, Jemalong [PDF]. For reasons that are obscure to me, the HapMap Project code to identify this line is the number 101.

Long before the genome sequence went to press, the next big project was already underway—sequencing the genomes of hundreds of barrel medick lines, to understand the complete diversity of the species. With the Jemalong genome as a starting point, collecting whole-genome sequences for other lines of the plant is quite a bit easier and cheaper. The HapMap Project now has (raw) sequence data for more than ten million genetic markers for almost 300 plant lines, from all over the native range—and a couple of places where barrel medick has been introduced.

2012.09.05 - First leaves Medicago truncatula—the "Jemalong" line. Photo by jby.
And this is more or less where I come in—last year I started a postdoctoral position in one of the labs collaborating on the HapMap Project at the University of Minnesota. The seeds sitting on my desk are from some of those 300 HapMap Project plant lines—and on a server in a building across the street from my office, there are some rather large files containing the genotypes, for those seeds, at millions of markers.

It's possible to grow up these seeds in the greenhouse, measure an interesting trait, and pair the measurements with that trove of genetic data to identify genome regions that are likely to be responsible for creating the trait. Or to delve into the sequence data and look for the fingerprints of natural selection across the entire species. Or to walk across the street and propose an experiment in the molecular biology of that trait to someone in a collaborating lab. The seeds on my desk are the nexus of a network of genetic data, trait variation, laboratory pratice, and natural history dating back millennia before humans first started building temples on Mediterranean islands.

Not bad for an unremarkable little wildflower.◼

References

Barker, D., Bianchi, S., & Blondon, F. 1990. Medicago truncatula, a model plant for studying the molecular genetics of theRhizobium-legume symbiosis. Plant Molecular Biology Reporter 8(1):40–49. DOI: 10.1007/BF02668879

Catoira, R., Galera, C., de Billy, F., Penmetsa, R. V., Journet, E. P., Maillet, F., Rosenberg, C., et al. 2000. Four genes of Medicago truncatula controlling components of a nod factor transduction pathway. The Plant Cell 12(9):1647–66. DOI: 10.​1105/​tpc.​12.​9.​1647

Cook, D., VandenBosch, K., Bruijn, F. de, & Huguet, T. 1997. Model legumes get the nod. The Plant Cell (March):275–282. DOI: 10.1105/tpc.9.3.275

Dart, P. J., & Day, J. M. 1971. Effects of incubation temperature and oxygen tension on nitrogenase activity of legume root nodules. Plant and Soil 35(1):167–184. DOI: 10.1007/BF02661849

Ellern, S., & Tadmor, N. 1966. Germination of range plant seeds at fixed temperatures. Journal of Range Management 19(6):341–345. JSTOR.

Penmetsa, R. V., & Cook, D. R. 2000. Production and characterization of diverse developmental mutants of Medicago truncatula. Plant Physiology 123(4):1387–98. DOI: 10.​1104/​pp.​123.​4.​1387

Pinto, C., Yao, P., & Vincent, J. 1974. Nodulating competitiveness amongst strains of Rhizobium meliloti and R. trifolii. Crop and Pasture Science 25:317–329. 10.1071/AR9740317

Robson, A., & Loneragan, J. 1970. Nodulation and growth of Medicago truncatula on acid soils, I: Effect of calcium carbonate and inoculationlevel on the nodulation of Medicago truncatula on a moderately acid soil. Crop and Pasture Science 21:427–434. DOI: 10.1071/AR9700427

Royal Botanic Gardens. 1889. Seeds of herbaceous plants. Bulletin of Miscellaneous Information 1889(26):29–56. JSTOR.

Ruegg, J., & Alston, A. 1978. Seasonal and diurnal variation of nitrogenase activity (acetylene reduction) in barrel medic (Medicago truncatula Gaertn.) grown in pots. Crop and Pasture Science 29:951–962. DOI: 10.1071/AR9780951

Simon, J. 1964. Inheritance of three marker characters in Medicago truncatula Gaertn. (= M. tribuloides Desr.). Crop and Pasture Science 16:31–36. DOI: 10.1071/AR9650031

Small, Ernest. 2011. Alfalfa and Relatives: Evolution and Classification of Medicago. NRC Research Press. Google Books entry.

Young, N. D., DebellĂ©, F., Oldroyd, G. E. D., Geurts, R., Cannon, S. B., Udvardi, M. K., Benedito, V. a, et al. 2011. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378):520–4. DOI: 10.1038/nature10625

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