Taking the <i>Phenomics Revolution</i> into the Field

摘要

The genomics revolution is racing ahead at full speed. Complete genome sequences now cost a fraction of what they were when the Human Genome Project started in 1990. The DNA in any plant variety influences how it will develop and grow in the face of multiple environmental challenges including soil type, weather, nutrition, and pests and diseases. Plant breeders can use this DNA information to associate the performance of plants, both in the greenhouse and the field, with the specific pieces of DNA carried by different varieties, even predicting performance before a seed is planted. But with all the power of current genotyping technologies, there is a limit to our ability to make strong connections between a plant's genes and its traits—our ability to measure the traits themselves. This situation is changing rapidly. Scientists around the world are making new connections among disciplines to develop and test technologies that can bring a data revolution to collecting plant phenotypes. And they are doing it in the most difficult and important environment—the field. Whether you are studying the basic biology of a plant, or breeding new crop varieties for farmers, the phenotype is the center of attention. Phenotypes are the physical characteristics of an organism, which result from its genes, environment, and how these two factors interact. A phenotype can be everything from the height of a plant, to its chemical composition, yield, or response to specific environmental factors. Long before the discovery of DNA and its role in heredity, farmers, breeders, and horticulturalists selected desirable plants based on the phenotype. Even with today's sophisticated genetic research, which regularly sees whole genomes published, it is what the genes do to the phenotype that matters. Measuring phenotypes of plants can be challenging. The subtle effects of genes that add up to determine quantitative traits can be easily missed and can require many repeated measurements to uncover. In addition, the structure of an entire plant can be difficult to quantify. Edgar Spalding, a professor in the Botany Department at the University of Wisconsin–Madison, says that compared with DNA sequencing technology, phenotyping technology is still rather crude. “It is not much of an exaggeration to say that a ruler is used, and that's not high throughput.” Spalding is a principal investigator for the Phytomorph project, which seeks to turn delicate developmental phenotypes into quantifiable measures. One of his new tools is a robotic camera that photographs growing seedlings and roots at regular intervals, with micron-level precision. His team tracks the root growth of Arabidopsis, maize, and tomato seedlings, looking for changes in their response to gravity. Images above by Erica Seccombe, courtesy of the High Resolution Plant Phenomics Centre. “Through electronic image capture and computer analysis, we can see how long even the tiny Arabidopsis root grows in five minutes,” Spalding says. “It may not be obvious, but in my view, when we have rich, high-throughput phenotyping, we are going to find out which component of that phenotype set has predictive power over something in the field.” Spalding stresses the importance of raising the capabilities of phenotyping tools. “Anything we can do to make the phenotyping activities more automated and more high throughput will make studies of genotype–phenotype relationships more effective. One of the new tools used by Edgar Spalding, principal investigator for the Phytomorph project at the University of Wisconsin–Madison, is a robotic camera that photographs growing seedlings and roots at regular intervals, with micron-level precision. “When was the last time you heard someone say that their phenotype data was wonderfully large and complex, but their genotype information needs more detail?” Phenomics, the study of complete phenotypes and how they change over time, is already underway. Companies such as Germany-based Lem