Corn Genomics: At the Touch of a Keystroke
The Maize Genetics and Genomics Database (MaizeGDB) is a web-accessible resource (www.maizegdb.org) that furnishes geneticists, breeders, and others with all things corn—from molecular markers and sequence data to genetic maps and bioinformatics tools for mining them.
“MaizeGDB puts data together in a way that would have taken researchers a long time to chase down and compile on their own,” says Carolyn Lawrence, a plant geneticist and MaizeGDB director at ARS’s Corn Insects and Crop Genetics Research Unit (CICGRU) in Ames, Iowa.
Launched in 1991 as “MaizeDB,” MaizeGDB is the product of many collaborators from CICGRU, ARS’s Plant Genetics Research Unit in Columbia, Missouri, ARS’s Plant Gene Expression Center in Albany, California, and cooperators worldwide. In addition to its support from ARS, MaizeGDB is also funded by the National Science Foundation and other organizations.
For all the powerful science behind it, MaizeGDB is surprisingly easy to use and offers straightforward explanations of key terminology—including how database information can be used.
For example, under a subhead titled “data centers,” clicking on the term QTL links the user to the following explanation: “A QTL (or quantitative trait locus) refers to a particular region of the genome that is associated with a particular trait. This association is made through statistical methods based on the counting and measurement of easily observed traits, such as the weight of 1,000 kernels, the height of the second leaf at a particular stage of development, and so forth.”
Conduct a QTL search for plant height and you get a list of experiments that evaluated plant height as well as links to the trait itself and 60 references describing it.
“At an early stage, the MaizeGDB team partnered with potential users to develop the database,” says CICGRU research leader Craig Abel. “The resulting feedback and the creativity of the MaizeGDB team to develop solutions have produced an exceptional genomic database.”
A recent noteworthy addition is a new genome browser that graphically displays sequence data for the inbred line B73. Another is the “Locus Lookup Tool.” According to Lawrence, this tool can help researchers locate specific genes that will help them develop a better corn plant. Ultimately, growers will benefit from this technology as healthier and higher yielding corn plants are developed.—By Jan Suszkiw, Agricultural Research Service Information Staff.
Carolyn Lawrence is in the USDA-ARS Corn Insects and Crop Genetics Research Unit, 1034 Crop Genome Informatics Laboratory, Iowa State University, Ames, IA 50011; (515) 294-4294.
"Corn Genomics: At the Touch of a Keystroke" was published in the September 2010 issue of Agricultural Research magazine.