The success of genome-sequencing projects highlights how little we know about how the whole organism is put together. Deciphering the relationship between the genome and the organism requires study of the effects of subtle genetic changes on the whole organism. This project will develop and apply one such approach by manipulating the expression of hundreds of genes and observing the effects on body shape, then using modeling to test understanding of how these effects occur. The project will focus on the genetic basis of shape of the wing of fruit flies, one of the few multi-cellular organisms where the necessary genetic manipulations are easy to accomplish and detailed data can be obtained in large quantities. This project has broad significance for biology, because health and disease in humans, improvement of domesticated plants and animals, and the ability of organisms to adapt, all derive from the relationship between the genome and the organism. This project will provide more detailed data on the genetic basis of variation in the whole organism than has previously been available. The research will provide a procedural model and analytical software which can be used by others to extend such studies to other organisms and that ultimately is applicable to humans and the species we interact with. Many undergraduates and a post-doctoral research will receive training through participation in this project.
Intellectual Merit: Form is the physical size and shape of an organism. When we look at the differences among related species, form changes gradually during evolution. The evolution of development must change to bring about the differences, but only in a subtle way. In contrast, much of our information about developmental variation is based on creating large alterations in development. For example, a very common experiment to verify that a particular gene has an effect on the development of some body part, is to essentially disable that gene and look for an effect. Such data does not necessarily tell us anything about variation relevant to small changes in form. In this project, we have measured the effects of subtle changes in development on the shape of the wing of the fruit fly Drosophila melanogaster. We did this by down-regulating each gene a variety of values between 10% to 75%. An example effect of down-regulating the gene brinker on wing shape is shown in Fig.1. These subtle changes are probably much more informative about the nature of natural variation that contributes to typical small and gradual evolutionary changes. We have manipulated well over 100 genes this way, and this allows us to describe the pattern of effects for the first time. Specifically we have found that our manipulations create variation in all the directions that are commonly found among fly wings in nature. Figure 2 shows how similar effects are for a sample of genes with large effects on shape. The fact that the lines point is all three directions shown suggests that many kinds of effects on shape are possible. The fact that the lines on Fig. 2 are fairly straight shows that most genes change just one aspect form. However, the rate of change in shape when expression changes is quite variable: sometimes a small change has a large effect on the wing, while sometimes there is no effect until gene expression has decreased a great deal. The effects on wing shape are not very well predicted by what is known about the function of a gene. The similarity of effects of ds, ft, ex and fj is an exception, as all four have large similar, effects on wing shape (since they all point to the right in Fig. 2), and all four are involved in the same developmental process. The data we have estimated in this project shows for the first time the relationship and magnitude of effects that small changes in gene expression have on the form of a part of the body. This will fuel our intuition about variation and evolution in other organisms, and help to predict the possible evolutionary paths that fly wings and ultimately other parts of other organisms may take in the future. Broader Impact: The broader impacts of this project are in two areas: training of the next generation of scientists, and the production and dissemination of software to facilitate analyses of similar data in the future. Much of the data collection on this project has been done by 34 talented and motivated undergraduate students, three graduate students and two post-doctoral researchers. Undergraduates have been involved in several roles. Twenty-four have been paid for their work rearing and measuring flies, processing of wing data, dissections, and general lab maintenance. Eight of these students also completed independent research projects. In addition, 10 other students did independent research projects for credit under the Florida State Directed Independent Study Program facilitated by this grant. The simplicity of the design of our experiments enables the students to both do original research, and to contribute to the overall project. The educational value of this for the students is tremendous. We have also updated our software to enable rapid measurement of fly wings (Wings4 and CPR), and have published LORY a program to enable visualization of differences in biological shapes from any organism. The software is freely available at http://bio.fsu.edu/~dhoule/Software/.
