(Posted Thu. Dec 19th, 2013)
Dec. 19: As the Maize Genetics and Genomics Database project moves forward, Off the Cob caught up with MGGDB 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 recruiting its first proteomics data set. While this is an ongoing effort, it should reach completion over the next few months. This data comes from a recently published paper in the prestigious journal Proceedings of the National Academy of the Sciences by a group of maize researchers at the University of California San Diego.
Gardiner begins with an explanation of what proteomics actually are.
“Scientists now know that the maize genome encodes about 40,000 genes that are the instructions for making proteins,” said Gardiner. “These proteins do the actual work of the cell; they are what actually make the corn plant grow and develop. Scientists refer to these approximately 40,000 proteins as the maize proteome.”
While it may seem logical that knowing the actual DNA sequence of maize would allow scientists to predict these proteins, he noted that is not the case.
“Sometimes, for reasons that are only partially understood, a different protein than one would have predicted from the DNA sequence is made,” he explained. “In other cases, the predicted protein is modified with a phosphate or sugar molecule and that completely changes what the protein does inside the cell. In both of these cases, the proteomics data helps us identify and understand these modifications and the protein’s new function.”
When added to the existing data at MGGDB, the new proteomics data will help maize researchers validate and understand the maize genome’s DNA sequence. He added that it would provide researchers with additional value as well.
“It provides an alternative perspective on what it takes for a corn plant to grow, develop and produce an ear,” said Gardiner. “In 1999, the National Corn Growers was instrumental in the establishment of the Plant Genome Research Program at the National Science Foundation. This research program would not have happened without the National Corn Growers and without it, the maize genome would never have been sequenced. This is very important because having the maize DNA sequence enables scientists to even entertain the idea of doing proteomics in maize-without the DNA sequence, proteomics would not even be possible.
“One way to think of the addition of this data is that the maize genomic DNA sequence is a Christmas tree that you have just put on the stand in your living room. When you add the lights and ornaments to the tree that is equivalent to adding the proteomics data to the genome sequence - each enhances the other to become something greater than either would have been alone.”
Gardiner concluded by explaining that the combined the genomics and proteomics data will give researchers a better chance of understanding complex traits like drought, yield, disease resistance and nutrient usage.
“Complex traits are very difficult traits to understand, and are even more difficult to manipulate to our advantage. If they were easy, this all would have been solved by now. Classical corn breeding has taken us a long way and will take us further if we are able to merge it with the newer molecular tools. This new proteomics data set represents another tool in the molecular plant breeders’ tool box. It will take time, but I am confident that we will get there. Just look at how far corn breeding has come in the last 100 years.”
To listen to the full interview, click here.