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Project Documentation & Protocols: Maize Gene Discovery Project: Education:
The Challenges of Maize Genetics

Contents: Maize Gene Discovery | The Challenge of Maize Genetics | Why Discover Maize Genes? | Finding Genes
Linking Genes to Function | Creating Databases | Building a Storehouse | Accomplishments | What's Next? | Glossary


The maize genome is BIG

Approximately 50,000 genes reside within maize's ten chromosomes. All told, these chromosomes contain about 2.5 billion base pairs -- the ladder steps of the DNA double helix. Thus, the maize genome is more than six times bigger than the rice genome (~400 million bases), and almost as big as the human genome (~3.2 billion bases).

The recently sequenced rice genome helps researchers understand maize genetics because the two plants share a common ancestor. But 60 million years of evolution separate the two cereals by thousands of genetic alterations as well as substantial changes in gene order and a six-fold expansion in genome size.


Subspecies genome size and organization varies greatly

Just as Chihuahuas bear little resemblance to Great Danes, corn subspecies vary greatly in appearance. In maize, these differences are accompanied by substantial differences in genome size and even gene order. Whereas dog genomes are more alike than they are different from one another, genomes of various maize subspecies vary in size by as much as 50%. To make matters more complex, contemporary U.S. corngrowers use a variety of hybrid seeds that are mixtures, in differing proportions, of two ancestral maize strains: northern flint and southern dent. Thus, there is no true-breeding, generally accepted standard of a corn plant genome. As a result, different maize geneticists have studied different subspecies and breeds.

To overcome this problem, the Maize Gene Discovery Project (MGDP) worked with multiple lines of corn and focused on finding genes rather than mapping them to a particular location in a specific subspecies. While other projects concentrate on placing genes on a chromosome map, the MGDP pays attention to finding genes and trying to understand their function.


Maize genomes contain multiple copies of most genes;

Like many plants, maize consists of the combined genes from several different ancestors, a condition known as polyploidy. Each chromosomal region generally has a duplicate on another chromosomal arm. Thus, the maize cell nucleus contains two or even four versions of identical or very closely related genes in different locations. Because of this redundancy, researchers cannot easily pursue a standard technique for gene discovery: "knocking out" a particular gene by mutation to see if it's essential to the plant's survival.

Rather than view maize's tetraploidy as a problem, the MGDP used it to advantage in its investigation of gene function. When a maize gene mutates, the plant will likely survive and provide clues as to the function of the mutant gene. In this way, maize mutants can generate information that would never be seen if there were but one gene encoding a crucial function. To exploit this fact, the MGDP created many mutant plants (learn more) and sequenced the mutated genes that might have caused the observed trait (learn more).


Jumping genes or transposons make up a large portion of the genome

Maize chromosomes are chockfull of transposons or retrotransposons, that have inserted many copies of themselves both inside genes and between them. At least 50% of the nuclear DNA of maize consists of long stretches of non-coding DNA made of retrotransposons nested within one another. Rather than sequencing these lengthy stretches of non-coding DNA, the MGDP focused on finding genes themselves using two targeted approaches (learn more).

For more information about the challenge of maize genetics, check out:

Background Information for the Maize Genome Effort:

Katherine Miller, a freelance science writer, contributed the text for this page to the Maize Gene Discovery Project. You can reach her at .

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