(Posted Wed. Mar 13th, 2013)
Mar. 13: 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 built upon how the increasing affordability of genome sequencing is allowing the scientists at the U.S. Department of Agriculture’s Agricultural Research Service-supported database to share the incredible amount of data being created in Ames, Iowa.
“The cost of DNA sequencing a maize genome has literally dropped from $30 million to sequence the first corn genome sequence to about $2,000 to $5,000 to sequence a corn genome today,” he began. “With two and a half billion DNA bases covering the ten chromosomes of maize, its genome is roughly about the size of the human genome, two and a half times the size of the soybean genome and about five times the size of the rice genome. With the amount of DNA sequencing happening now, we are developing an appreciation for all of the small DNA sequence changes between two corn varieties which we call single nucleotide polymorphisms or SNPs.”
Gardiner explained that while the title single nucleotide polymorphism may not be familiar to some, it is an easily accessible concept.
“A single nucleotide polymorphism, or SNP, is a change at a single DNA base,” he explained. “Remember from your high school or college biology class that DNA is made up of four bases, A, T, G or C, which form a long chain to become a chromosome. The maize genome has about two and a half billion of these A, T, G, or C’s. A SNP is a change at one of these two and a half billion DNA bases. It turns out that maize has lots of SNPs with about one base per 100 bases differing between any two corn varieties. Every corn line actually has millions of these small changes, or SNPs, when compared to another corn variety. Many of these SNPs have no effect on the plant, but a small number of them can have dramatic effects on the corn plant.”
Gardiner then went on to explain not only what the project does with the ability to compare these differences but also why this is important.
“Our overall goal is to make this information accessible to the researcher via the MaizeGDB website, but this is really quite challenge mainly because of the amount of data with which we are dealing,” said Gardiner. “In 2009, the B73 maize genome sequence was completed to a very high level of accuracy. This genome became the maize genome reference sequence, essentially the ‘gold standard’ for corn. This was really made possible by the National Corn Growers Association’s efforts to help establish the National Science Foundation’s Plant Genome Research Program in 1998. By 2011, advances in sequencing technology had increased the number of maize varieties to 27 with one and a half million SNPs. By 2012, the number of lines had increased to 103 with 55 million SNPs. Things are moving very quickly, and we expect to have 100,000 lines with about 100 million SNPs per line in the near future.”
Given the massive amount of data, MaizeGDB works to develop tools to help researchers locate the information necessary for their work in a more time and cost efficient manner.
“This volume of data challenges the capabilities of your typical relational database,” explained Gardiner. “This data comes from the USDA-ARS as well as projects funded by the National Science Foundation. In the future, we also expect to be receiving data from the International Maize and Wheat Improvement Center located in El Batan, Mexico. To make that data more useful, we are employing strategies that allow us to preselect the lines or specific chromosomal regions in which we are interested. These software tools (developed by Mark Millard) allow us to focus in on a narrower slice of the data, thus making it more manageable.”
Gardiner then explained that SNPs can also be used for direct comparison between corn genomes thus showing the differences which have developed and how closely they may be related. While progress is still ongoing, the work being done will result in a tool which aides researchers in their work providing America’s corn farmers with high yielding, sturdy seed varieties that can thrive even in less than optimal conditions.
To listen to the full interview, click here.