Amaizing: Corn Genome Decoded
News Nov 20, 2009
In recent years, scientists have decoded the DNA of humans and a menagerie of creatures but none with genes as complex as a stalk of corn, the latest genome to be unraveled.
A team of scientists led by The Genome Center at Washington University School of Medicine in St. Louis published the completed corn genome in the Nov. 20 journal Science, an accomplishment that will speed efforts to develop better crop varieties to meet the world's growing demands for food, livestock feed and fuel.
"Seed companies and maize geneticists will pounce on this data to find their favorite genes," says senior author Richard K. Wilson, Ph.D., director of Washington University's Genome Center, who led the multi-institutional sequencing effort. "Now they'll know exactly where those genes are. Having the complete genome in hand will make it easier to breed new varieties of corn that produce higher yields or are more tolerant to extreme heat, drought, or other conditions."
Corn, also known as maize, is the top U.S. crop and the basis of products ranging from breakfast cereal to toothpaste, shoe polish and ethanol. The corn genome is a hodgepodge of some 32,000 genes crammed into just 10 chromosomes. In comparison, humans have 20,000 genes dispersed among 23 chromosomes.
The $29.5 million maize sequencing project began in 2005 and is funded by the National Science Foundation and the U.S. departments of agriculture and energy. The genome was sequenced at Washington University's Genome Center. The overall effort involved more than 150 U.S. scientists with those at the University of Arizona in Tucson, Cold Spring Harbor Laboratory in New York and Iowa State University in Ames playing key roles.
The group sequenced a variety of corn known as B73, developed at Iowa State decades ago. It is known for its high grain yields and has been used extensively in both commercial corn breeding and in research laboratories.
The genetic code of corn consists of 2 billion bases of DNA, the chemical units that are represented by the letters T, C, G and A, making it similar in size to the human genome, which is 2.9 billion letters long.
But that's where much of the similarity ends. The challenge for Wilson and his colleagues was to string together the order of the letters, an immense and daunting task both because of the corn genome's size and its complex genetic arrangements. About 85 percent of the DNA segments are repeated. Jumping genes, or transposons, that move from place to place make up a significant portion of the genome, further complicating sequencing efforts.
A working draft of the maize genome, unveiled by the same group of scientists in 2008, indicated the plant had 50,000-plus genes. But when they placed the many thousands of DNA segments onto chromosomes in the correct order and closed the remaining gaps, the researchers revised the number of genes to 32,000.
"Sequencing the corn genome was like driving down miles and miles of desolate highway with only sporadically placed sign posts," says co-investigator Sandra Clifton, Ph.D., of Washington University. "We had a rudimentary map to guide us, but because of the repetitive nature of the genome, some of the landmarks were erroneous. It took the dedicated efforts of many scientists to identify the correct placement of the genes."
Interestingly, plants often have more than one genome and corn is no exception. The maize genome is composed of two separate genomes melded into one, with four copies of many genes. As corn evolved over many thousands of years, some of the duplicated genes were lost and others were shuffled around. A number of genes took on new functions.
Corn is the third cereal-based crop after rice and sorghum – and the largest plant genome to date – to have its genome sequenced, and scientists will now be able to look for genetic similarities and differences between the crops. "For example, rice grows really well in standing water but corn doesn't," explains co-investigator Robert Fulton, of Washington University. "Now, scientists can compare the two genomes to find variations of corn genes that are more tolerant to wet conditions."
The United States is the world's top corn grower, producing 44 percent of the global crop. In 2009, U.S. farmers are expected to produce nearly 13 billion bushels of corn, according to the U.S. Department of Agriculture.
U of M plant scientist uncovers clues to yield-boosting quirks of corn genome
When it comes to corn, 1 + 1 = more than 2: The offspring of two inbred strains tend to be superior to both of their parents. Characterizing the gene-level variability that leads to this phenomenon, known as heterosis or hybrid vigor, could boost our ability to custom-tailor crops for specific traits, such as high protein content for human consumption or high glucose content for biomass fuel.
With help from the newly released DNA sequence of the common corn strain B73, University of Minnesota plant biologist Nathan Springer and colleagues from Iowa State University, Roche NimbleGen, and the University of Florida have begun doing just that—and come up with some surprising findings.
In a study reported in the Nov. 20 issues of Science and PLoS Genetics, the researchers compared the genetic sequence of B73 with that of a second inbred strain, Mo17. They discovered an astonishing abundance of two kinds of structural variations between the pair: differences in the copy number of multiple copies of certain stretches of genetic material, and the presence of large chunks of DNA in one but not the other. In fact, at least 180 genes appearing in B73 aren't found in Mo17, and Springer, an associate professor of plant biology in the College of Biological Sciences, suspects that Mo17 likely has a similar number of genes that B73 lacks.
"The genomes of two corn strains are much more different than we would have thought," Springer said. "What struck us is how many major changes there are between two individuals of the same species."
The researchers think that this diversity, which is almost as great as the difference between humans and chimpanzees, is what's behind the superiority of hybrids. When the genetic material from the two very different parents combines, the offspring end up with more expressed traits than either parent - the best of both worlds, gene-wise.
The findings are important because corn is important. Domesticated some 10,000 years ago, the crop produces billions of bushels of food, feed, and fuel feedstock each year in the United States alone. If we understand the molecular underpinnings of hybrid vigor, Springer says, we can potentially produce true-breeding lines of corn with specific traits for specific uses.
In treating inflammatory bowel disease (IBD), physicians can have a hard time telling which newly diagnosed patients have a high risk of severe inflammation or what therapies will be most effective. Now researchers report finding an epigenetic signature in patient cells that appears to predict inflammation risk in a serious type of IBD called Crohn’s disease.