DATABASE HELPS RESEARCHERS VISUALIZE MAIZE GENOME

NOVEMBER 2012

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(Posted Wed. Nov 14th, 2012)

Nov. 14: This week, Off the Cob caught up with Maize Genetics and Genomics Database Curator Jack Gardiner to find out how the project has progressed over the past three months.  The MGGD, which is supported by the U.S. Department of Agriculture’s Agricultural Research Service, is a tool being developed with assistance from the National Corn Growers Association. When complete, it will help scientists efficiently apply the knowledge gained from the Maize Genome Sequencing project to develop varieties that perform for farmers in the field.

 

“Recently, we have been working on ways to visualize new sequences of the maize genome that we know are currently being developed in the maize research community,” Gardiner began. “We call these alternative genome sequences.”

 

While the term alternative genome sequences may not be familiar to many, he explained it holds a very specific meaning in the research community.

 

Alternative genome sequences basically represent complete genome sequences of other corn varieties besides the B73 variety that was sequenced in 2009,” he said. “B73 was a very good choice for the first genome to be sequenced, but it clearly does not represent all genomic diversity found in maize.  No single maize inbred could do this.”  

 

Gardiner went on to explain that, while genome sequencing is commonly perceived as quite expensive, the cost to carry out a project of this nature has come down substantially over the past decade.

 

“Genome sequencing used to be very expensive but that is rapidly becoming a thing of the past,” said Gardiner. “B73, the first variety sequenced with the help of the National Corn Growers and the support of the National Science Foundation’s Plant Genome Research Program, cost about 30 million dollars. Without NCGA’s support of this National Science Foundation Program, complete sequencing of the maize genome would never have happened. Now, depending on the quality of the DNA sequence, you can do it for about five thousand dollars.  We know that there are currently thousands of corn varieties being sequenced by a variety of research groups.  At Maize GDB, we are working on ways to visualize these hundreds of complete genome sequences that will become available in the next few years. No longer is the challenge generating the information but rather presenting the information in a way that is easy to understand.”

 

   

 

To listen to the full interview, click here.