Plant functional genomics: beyond the parts list.

Although one might infer something about how a supersonic jet aircraft flies by identifying all its parts, it would help to know how all the parts fit together to produce a functional machine. Now that two plant genomes have been fully sequenced, and many genes have been identified for other plant species, we are in the midst of understanding how all the parts interact to produce a plant – in other words – functional genomics. I personally have never been too enamored of simply identifying parts. As an avid British car enthusiast, I enjoy tinkering in the garage (it helps particularly to understand electrical circuits) to improve, or at least maintain, an old automobile. Identifying a bunch of parts on the garage floor is not as enjoyable as tinkering. Functional genomics is the fun part of the science in my view – the integrating science behind the special endowments of plants that not only endear these organisms to plant scientists but also have important roles in feeding the world.The four functional genomics papers in this special tenth anniversary issue of Trends in Plant Science illustrate the globalization and increasing accessibility of the science, which is a fairly recent development in its own right. Unlike high-energy physics, which has always been and always will be expensive, the cost of genomics research has decreased [1xGenome sequencing in microfabricated high-density picolitre reactors. Margulies, M. et al. Nature. 2005; 437: 376–380Crossref | PubMed | Scopus (4378)See all References[1]. It should not be surprising to see it being used for crop improvement to help feed the world's poorer people, the theme of this issue of Trends in Plant Science.In this issue, Willem Rensink and Robin Buell focus on expression profiling as a functional genomics tool. In microarrays, we see a classic case of gradual affordability. Over the past 7 years, the cost of doing a microarray experiment has decreased by an order of magnitude, whereas the information on an array has increased threefold, at least for Arabidopsis thaliana, making this technique much more accessible to the typical researcher. Along with the initial high costs, there were also fears that microarray experiments would not be replicable, but recently it has been shown that the data are fairly robust; not perfect, but not as problematic as originally predicted [2xIndependence and reproducibility across microarray platforms. Larkin, J.E. et al. Nat. Methods. 2005; 2: 337–343Crossref | PubMed | Scopus (319)See all References[2].Rice is perhaps the most important crop on earth, and in this issue Yonghong Wang shine a light into China to discuss how scientists there are using biotechnology and genomics to improve this staple crop. The modest size of the rice genome is advantageous and the resources available are tremendous. One aspect of these resources, not exclusive to rice of course, is the burgeoning of databases interconnected via the internet. Indeed, it would be difficult to imagine genomics without the internet, which has greatly increased the utility of bioinformatics to the practicing geneticist – particularly in developing countries.One condition that continues to plague mankind, particularly some of its poorest members, is soil salinity. Here, Toshio Yamaguchi and Eduardo Blumwald describe research progress towards the production of salt-tolerant plants. Specifically, marker-assisted breeding and QTL identification coupled with transgenic approaches are likely to provide stable solutions to an ever-growing problem. In this example, we see how functional genomics has built upon the foundation of biophysics research involving transporters and antiporters to better understand how the genome of a plant might be manipulated to increase its salt tolerance. This example shows how functional genomics ‘stands on the shoulders of giants.’Finally, we have a paper by Rajeev Varshney on genomics-assisted breeding as a method to improve crops. They provide a list of bioinformatics resources and databases useful for using genomics in breeding. In addition, they go beyond marker-assisted selection to describe how gene expression data might be useful in crop breeding. In particular, they discuss the future of expression QTL (eQTL). Expression profiles can be mapped and added to the information needed to understand trait development in plants. This example illustrates the trend of in silico biology becoming as important as bench-top biology.Amongst all the clatter about the post-genomic age and the waning excitement over completed genome sequencing of humans and now plants, I think the best is yet to come. We are (thankfully) passed the era where a millionaire genome guru has sequenced his own DNA, and onto an exciting time where genomics information can actually be applied to benefit agriculture and food production: egalitarian agrarian biology. Also thankfully, it is not only rich laboratories in ivory towers who are participating in the discoveries that will benefit the world. Indeed, some of the best work is being performed in developing countries because their governments have chosen to invest in facilities and scientists in this key area of functional genomics. The trend is pointing toward more collaboration and sharing of data and materials across national boundaries, with open source biology potentially leading the way into future discoveries. Among all the biological sciences, perhaps functional genomics and mankind have the most to gain from this trend.