(Posted Thu. Jun 6th, 2013)
Jun. 6: As the Maize Genetics and Genomics Database project moves forward, Off the Cob caught up with MaizeGDB Curator Dr. Jack Gardiner for an update on the progress made over the last quarter. In the interview, Gardiner explained how the U.S. Department of Agriculture’s Agricultural Research Service-supported database in Ames, Iowa has been refining descriptions of maize phenotypes and thus making them more consistent with how other groups describe and classify phenotypes.
Gardiner began by explaining what the difference between a genotype and a phenotype actually is and providing examples of how one might distinguish between the terms.
“When we say genotype, we are referring to the inherited instructions that are specified by an organism’s genetic code or DNA sequence,” Gardiner explained in reference to the way in which scientists use this terminology. “Genotype can refer to either a single gene or the entire set of genes in an organism. When we say phenotype, we are referring an organism’s observable characteristics, such as color, shape or size, or as a result of an indirect measurement process, such as its biochemistry or behavior. Roughly speaking, a plant phenotype describes a plant trait. For example, the maize Opaque2 (O2) gene on chromosome 7 was identified on the basis of its mutant phenotype. That is, corn kernels that have a mutant copy of the O2 gene have an opaque or chalky-whitish appearance that makes them easy to identify on the ear when compared to kernels with a functional copy of the O2 gene. It turns out that mutant O2 kernels also have higher amounts of lysine and tryptophan, two amino acids which are typically low in maize. Maize has about 1,100 phenotypes which have been described. Maize phenotypes typically have names like narrow leaf, defective kernel, yellow seedling, tassel seed, dwarf plant, or blotched leaf. We know the actual gene that specifies the phenotype, but for most, we have no knowledge of the gene that specifies the phenotype.”
He went on to explain the importance of the way in which a scientist describes maize phenotypes.
“In our past conversations, I have described MaizeGDB’s overall goal as one of making information accessible to maize researcher via the MaizeGDB website. I think we can all appreciate the hard fact that information is not of much use if you can’t retrieve it easily. If you can’t find it, you might as well not have it,” said Gardiner. “There are many other plants and animals that are studied in the same level of detail as maize, and they all have biological databases and face many of the same data organization and retrieval issues as maize. What scientists want to avoid, as much as possible, is having each group reinventing their own wheel. Harmonizing how we describe phenotypes across different biological databases just makes sense from an efficiency standpoint, but it also has another very important feature in that it allows the different biological databases to exchange information in a way that would not otherwise be possible. We definitely know that there are other phenotypes that are observed in other plants, like rice or sorghum, which are useful to researchers working on maize. What we want to be able to do when we describe maize phenotypes is position ourselves to capture as much information as possible about phenotypes in other plants and even animals in some cases.”
Gardiner then described how MaizeGDB is going about this task of organizing its phenotype information to improve their ability to take advantage of what is known about phenotypes in other plants.
“To refine how it describes maize phenotypes, MaizeGDB has joined a research collaboration network. This Phenotype RCN is supported by the National Science Foundation and was established to help develop standardized ways to describe phenotypes in both plants and animals. The Phenotype RCN is essentially a community of about 300 scientists that are interested in comparing phenotypes across plants and animals and are working to develop analysis tools to make this possible. There are researchers from soybean, tomato, rice and other crop plants involved in this collaboration.
“The first order of business for any member of the Phenotype RCN was to convert a small set of phenotype descriptions into a new format for describing phenotypes that would allow phenotypes to be compared across different plants and animals. MaizeGDB focused on about 300 phenotypes where we knew the gene that specified the trait. This data has been submitted to the RCN project coordinators and is currently being analyzed to see if the RCN’s approach to harmonizing phenotypes across different plant and animal species is a workable approach. Ideally, we would like to be able to look at a phenotype or trait in one plant species like rice or sorghum, and make a prediction as to what that phenotype or trait would look like in maize.”
Gardiner went on to speak about possible future NCGA work with phenotypes and how these efforts could benefit the entire industry.
To listen to the full interview, click here.