Genomic Analysis of Seed Quality Traits in Corn

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About 85% of the U.S. corn harvest is used as animal feed, therefore the development of "high energy feeds" is highly relevant to the economy of the United States. Fats are the most concentrated source of energy in the cell. The long term effort conducted at the University of Illinois has resulted in lines with about 20% oil (Illinois High Oil or IHO) as well as lines with less than 2% oil (Illinois Low-Oil or IHO). These lines have retained a very high level of genetic diversity and preliminary mapping studies suggest that a large number of genes are involved in this important trait. The goal of the research is to identify all of the genes that are involved in this genetic trait.This research program will use a "candidate gene approach" to identify genes that may play a significant role in oil deposition in corn. The first step of this approach consists of using parallel gene expression analysis as a tool to identify genes whose expression levels are altered in IHO vs ILO maize. By using the large collection of maize mutants with defects in embryo and endosperm development it should be possible to identify a large number of genes that share common developmental expression programs. A number of maize lines have also been found that can "modify" the amplitude of the IHO trait (i.e., lines of corn that contain modifier genes for the IHO genes). These lines of maize could also be useful in finding candidate genes associated with components of the high oil traits.The aforementioned approach will identify many candidate genes. To reduce this number of candidates to a smaller number of "highly probable" candidates genes, a number of strategies will be used to map single gene mutations relative to the high oil trait. These will rely on cutting edge mutation detection technologies. Two strategies will be used to associate single nucleotide mutations and components of the high oil trait:The first will consist of a "direct association" between single nucleotide mutations and components of the high oil trait.The second will consist of an "indirect association" between single nucleotide mutations and IHO genes.Both of these strategies will exploit the plant genetic resources developed by the University of Illinois for high resolution mapping of DNA polymorphisms in IHO x ILO crosses.In addition to the research goal, this research program is designed to train graduate students and post-doctoral fellows in the science of genomics. The students will have the benefit of having two thesis advisors each and each PI will serve as a co-advisor to a minimum of 2 students.