Rice was the first grass to have its genome sequenced and published, which wouldn’t have been possible without the government and private industry’s massive efforts to decode the human genome. The sequencing and analysis of genes, human or sorghum, revealing the arrangements of hundreds of millions of DNA bases, is a great scientific accomplishment, but researchers say this is just the beginning. What follows is the mapping of genomes from many more varieties. After that, a tremendous amount of work still remains in figuring out what it all means.

All humans have largely the same set of genes, but look around and vast disparities in people’s physical features can be observed. Many of mankind’s physical differences are traced back to the geographic origin of a population, but what are the genetic mechanisms at play behind these mysteries of variation? To answer this question, scientists are working to profile an array of human genomes from the most geographically diverse regions on the planet in hopes of better understanding how particular variations in genes cause specific physical qualities in humans. The purported big payout for humanity is better disease treatment and prevention.

To better understand the drought-tolerant sorghum plant, research is moving forward in much the same way. However, whereas knowledge in human genetics is expected to stay within ethical boundaries by helping prevent disease and increase the quality of life, plant and crop breeders seek the identification and exploitation of sorghum’s beneficial characteristics to enhance yields and reduce input requirements for future commercial crops, including dedicated varieties for advanced ethanol production.

“The beauty behind having this kind of information available is that we’ll be able to tailor plants to the particular needs of a biorefinery, just based on the information provided by those plants and our knowledge of how these genes are working in sorghum,” says Jeff Dahlberg, research director for the Lubbock, Texas-based United Sorghum Checkoff Program. The newly established checkoff will pay for sorghum information, education and research campaigns. “One of the unique things about sorghum is that it’s a crop that fits all the different models for renewable fuels right now,” Dahlberg says. “We produce grain sorghum, and we’re already in the grain-to-ethanol market. About 18 [percent] to 20 percent of our domestic sorghum production is going into the grain-to-ethanol market.” Sorghum is the No. 2 crop used for grain-based ethanol production in the U.S., and grain sorghum ethanol counts as an advanced biofuel under the new renewable fuels standard or RFS2. According to Tim Lust, executive director for the National Sorghum Producers, 2009 will be the first year ethanol has taken first place in terms of domestic markets for grain sorghum. “Domestically, the hog and beef cattle industries have historically held that role, but ethanol will surpass that this year,” Lust says. In 2008, producers planted close to 8.3 million acres of grain sorghum.

There is also a forage variety of sorghum, which Lust says accounted for about 5 million acres planted in 2008. “And then we have sweet sorghums, which are unique types of sorghums,” Dahlberg says. “They not only produce grains, but also stem juices which are high in sugars—almost as high as sugarcane.”

Sorghum and sugarcane are very closely related, along with Miscanthus and one of the world’s most hated weeds, Johnsongrass. Dahlberg says a high grain, high sweet-stemmed biomass sorghum would be an ideal biocrop.

The Methodology of Sequencing
Mapping out a genetic blueprint involves determining several short sections that would make up a gene, and sequencing those in bulk. Then, scientists take all of those pieces and put them together like a puzzle—a difficult puzzle, according to Dan Rokhsar, the computational biology leader at the U.S. DOE Joint Genome Institute in Walnut Creek, Calif. “There are parts of the genome that are very complicated to assemble,” Rokhsar says. “Think of them as large stretches of blue sky in a puzzle, with wispy clouds throughout. So, you have to use that cloud information to put together those regions of the genome.” As the puzzle starts to take shape, he says the reconstruction of entire genes and eventually whole chromosomes takes place.

Rokhsar says the JGI employs an almost factory-like setting to gene sequencing, using 50 sequencing instruments into which material is fed day and night. “It’s a big assembly line,” he says. The sequencing process itself took about four months, Rokhsar says. That data is then made available in digital form and worked on by researchers such as John Bowers of the University of Georgia; Jeremy Schmutz of the DOE JGI Hudson Alpha Institute for Biotechnology; and Andrew Paterson, director of the plant genome mapping laboratory at the University of Georgia. Rokhsar tells EPM that those researchers, along with others, are doing a “relatively customized assembly process.”

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