Maize Genetics and Genomics Database Expert Talks SAM, New ProjectsThu, 22 May 2014 11:52:01 CDT
As the Maize Genetics and Genomics Database project moves forward, Off the Cob, a production of the National Corn Growers Association, caught up with MGGDB Curator Dr. Jack Gardiner for an update on the progress made over the past few months. In the interview, Gardiner explained the newest project that the U.S. Department of Agriculture's Agricultural Research Service-supported database in Ames, Iowa, has undertaken to develop translational data. (You can hear that interview by clicking on the LISTEN BAR at the bottom of this story.)
Gardiner begins with an explanation of what translational data actually is.
"We always have lots of projects to choose from at MaizeGGDB. So, we try to focus on projects which will be of most use to our user community, which is primarily composed of maize breeders and geneticists," said Gardiner. "Since we are primarily supported by the USDA-Agricultural Research Service and the National Corn Growers, we try and further narrow our focus on data sets that we hope will translational. By translational, I mean data sets that will hopefully translate into real world solutions such as developing hybrids that utilize water, sunlight and nutrients more efficiently."
With this in mind, Gardiner describes the new project MaizeGGDB has undertaken.
"We are initiating a National Science Foundation-supported, four-year curation project to take in data from a multi-institutional group of researchers from Cornell University, Truman State University, Iowa State University, University of Minnesota, Kansas State University, University of Georgia and Cold Spring Harbor," he explained. "The data that will be curating over this period is on the maize shoot apical meristem, a cluster of cell deep inside the young maize seedling. The maize shoot apical meristem in the 14-day-old seedling is a cluster of about 1,500 cell that ultimately gives rise to all above ground parts of the maize plant. As you can imagine, it is very tiny, and you need a microscope to see it. We refer to the maize shoot apical meristem as SAM for short."
Then, he explains what SAM in greater detail.
"The shoot apical meristem, or SAM, starts as a cluster of about 250 'founder' cells that are destined to become all above ground parts of the corn plant, the leaves, stems, ear, tassel and, well, everything," said Gardiner. "In the 14-day-old maize seedling, those 1,500 SAM cells have already started to undergo specialization."
Given the incredibly small size of SAM, he explains researchers only recently developed the ability to study it.
"This is why it takes a multi-disciplinary team; there are just so many areas of expertise that are needed to make a project like this work. In this particular project, they have benefitted from technical advances in microscopy and sequencing technology. Using computer-assisted tomography, otherwise known as a CAT scan, they are able to create a 3D image of the SAM. Then, they can use a laser to dissect the SAM into specific regions and actually capture those regions for sequencing. This allows them to determine what genes are turned on in those regions. This type of work just wasn't possible ten years ago.
"The group will take several complementary approaches to understand how the SAM works and its potential for manipulation to produce maize lines with desirable agronomic traits. First, they will take 3D CAT scans for about 380 diverse maize lines to develop high resolution, 3D images of the maize SAM at 14 days.
"Because maize has so much genetic diversity, the size and shape of the maize SAM actually varies significantly among different maize inbred lines. It is interesting to note that the size and shape of the maize SAM is affected by the growing conditions.
"Next, the group will use gene-mapping techniques to identify the genes that control the size and shape of the SAM and its response to planting densities."
Gardiner concluded by explaining why he believes knowing the genes that affect the size and shape of the SAM, and its response to different planting densities, will translate into to maize varieties that are better able to utilize sunlight, nutrients and water more effectively.
"It is generally accepted in the plant breeding community that development of maize varieties that can thrive under increased planting density account for a large part of the gains in yield achieved over the past 100 years. This was possible as corn breeding allowed us to develop maize varieties that can better capture sunlight in a smaller volume of space. In previous work, this group established that the size and shape of the SAM has a strong correlation to leaf width, leaf length, leaf number and stem width, all of which are agronomically important adult plant traits.
"It seems reasonable to assume that a better understanding of the genes that control the size and shape of the SAM will lead to a better understanding of phenotypic traits that determine the overall architecture of the mature corn plant. Once identified, these traits can be selected for early on in corn breeding programs and thus speed up the development of new hybrids. In research, you never know where your chosen path is going to take you, but if the past is a predictor of the future, you can have faith that eventually you will end up in a better place than you were at before. This is why research is so fundamental to any forward-looking society, and always will be."
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