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Gene Atlas Project Looks to Identify Gene Function

Posted Jun. 30, 2009

As part of our mission to benefit farmers and ranchers, the Noble Research Institute works to improve vital grasses and legumes through traditional breeding and scientific research.

Alfalfa is one of the forage species we work with because of its vital nature to agricultural production. Alfalfa is the United States' third most valuable crop after corn and soybean, and contributes more than $8 billion annually to the national economy.

The Noble Research Institute's scientists began looking to improve alfalfa in the early 1990s, but it has a complex genome (all the genes in an organism) that makes it a poor species for genetics and genomics research.

Through the last decade, the Noble Research Institute has expended considerable time, effort and funding to use a closely related legume, Medicago truncatula (commonly called barrel medic), as a research tool for understanding more complex legumes that are economically and agronomically important. The Noble Research Institute's scientific divisions search for genes within Medicago that control functions important for agricultural production, such as forage quality and digestibility, disease and insect resistance and tolerance, as well as abiotic stresses, such as drought and soil acidity. If we can understand a gene's role within a plant, we can potentially use it to increase crop productivity or, alternatively, to reduce the need for expensive inputs.

My laboratory looks at the functions of genes within a plant's organs - roots, stems, leaves, flowers and seeds. To begin the challenging project of cataloging and comparing the tens of thousands of genes, we developed the Medicago Gene Expression Atlas (or "gene atlas"), a massive database identifying genes and their associated function(s).

The gene atlas shows us which genes are active (or "expressed") in a particular organ and when they are active. It's like watching football. The genome of a plant is the team roster of a football team, and the genes are the individual players. The gene atlas shows where and when genes are playing, and what other genes they're playing with - imagine a snapshot of a football field at a particular point in a game. Scientists can learn a lot about who's playing and their interactions with other genes.

The ability to know which genes are active at a particular stage of plant development allows us to hypothesize about the gene's functions. If certain genes are expressed in the leaves, for example, then we might hypothesize that they play a role in photosynthesis.

As important as individual gene activity, my laboratory also looks for proteins called "transcription factors." Transcription factors act like coaches controlling teams of genes. There are upwards of 2,000 transcription factors in Medicago, each controlling 20 to 30 genes on average. Understanding these proteins is important to our achieving better understanding of individual gene function.

Currently we perform our research under ideal circumstances, providing plenty of water, nutrients and light, and protection from outside influences. Rarely in agriculture does a plant have greenhouse-quality conditions, so we are also exploring what genes become active when they experience environmental stresses. When a plant is challenged by factors such as drought, pest attacks or pathogen invasions, genes activate as part of a safeguard mechanism.

Many genes are expressed at low levels, or set to "idle," until they are really needed because expressing them to their fullest costs the plant significant energy. If we can determine which genes respond to an environmental stress like drought, we can better understand the plant's process of coping with the problem. In turn, we can breed new varieties with enhancements to specific genes, making a plant more drought tolerant for instance.

As Medicago is a model, the knowledge that we are creating has a broad application. Noble scientists are already applying our research with Medicago to alfalfa, but we understand that its application is useful to a multitude of crops around the world.