(Posted Wed. May 2nd, 2012)
May 2: Today, the National Corn Growers Association’s “Off the Cob” podcast series speaks with Dr. Jack Gardiner, the curator of the Maize Genome and Genetics Database, where NCGA has funded activities that will add functional genomic software tools into the preexisting USDA ARS database. When completed, these tools will allow researchers to easily isolate and examine manageable data sets, thus decreasing the time and effort needed to utilize the massive amounts of genomic data on corn and produce results that will aid farmers.
The work on the Maize Genome and Genetics Database continues NCGA’s leadership in the area of corn genetics. Instrumental in its role as a proponent of the original Maize Genome Sequencing Project, the organization continues service to growers in its work bringing together the scientific talent and funding needed to advance collective knowledge supporting innovation.
As work toward this eventual goal chugs along, Gardiner provides an update on the project’s progress while delving more deeply into how this tool, and the science that it makes more easily usable, looks to a trained scientist.
“One of the major challenges scientists face when looking at the incredible wealth of information gained through the sequencing of the maize genome is how to reduce the data and simplify it so that it can be examined in a meaningful manner,” he said. “Through a collaboration with the University of Toronto, we have developed a tool called the EFP browser. Based upon the group’s existing tool and customized to better suit the needs of maize researchers, the EFP browser focuses on analyzing gene expression data.”
Gardiner went on to explain what precisely this means and how it helps in the development of products that matter to farmers.
“Maize has, roughly 40,000 genes. On any given part of the corn plant, not all of the genes are on and not all are off. Instead, it is an interesting blend of the two,” he explained. “As a rule of thumb, in a maize plant approximately half of the genes, or approximately 20,000, are on, meaning that they are actively expressing themselves. The EFP browser helps scientists visualize what maize genes are actually on or off and thus causing a certain physical expression. ”
Gardiner notes that these tools, in essence, fine tune the process of locating the genetics that help researchers pinpoint how to select for develop traits that growers want.
“The EFP browser displays information on which genes are on and off in a picture that helps a research take an actual look at what is making something expressed in the actual plant,” he explained. “In showing how active each gene is in a particular tissue, this tool expedites the ability to isolate the genes causing a favorable trait in corn thus more quickly enabling a move toward developing seeds capable of consistently demonstrating this strength.”
As progress continues, Gardiner hopes to share both images and explanations of the cutting-edge tools that will help researchers develop the seeds farmers need more efficiently.
To take a quick tour of the EFP browser, complete with actual images and Gardiner’s explanation, click here.
To listen to the full interview, click here.