Unraveling the Mysteries in Sorghum's ‘Simple' Genome

Grain sorghum's genome is about a fourth the size of man's, and much less complex than other related grasses. Now that its genetic blueprint has been published, EPM asks scientists and sorghum experts what this means for science, agriculture and advanced ethanol production.
By Ron Kotrba | April 14, 2009
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."

Paterson says the University of Georgia definitely took advantage of the rice sequence to refine sorghum's. "We knew from genetic maps that rice and sorghum had pretty similar genomes," Paterson says. "There weren't large numbers of chromosomal rearrangements, so as the assembly of the sequence was built, it was natural for us to kind of compare sorghum to rice. And where we found something different we scrutinized it. We couldn't assume the differences were wrong, but we certainly could add an additional level of skepticism to inspecting them." Paterson says he believes this scrutiny has led to what appears to be a very high-quality sequence for sorghum.

A chromosomal sequence consists of a string of four nucleic acid bases—A (adenine), C (cytosine), G (guanine) and T (thymine)—arranged in various orders making up DNA. Figuring out which parts of the DNA represent genes, however, is no small task. At least half of the sorghum genome is made up of sequences that are not really related to genes. These sequences were once called "junk DNA," but the more neutral term favored today is "repetitive elements"—sequences of DNA repeated hundreds of thousands of times in the genome but aren't thought to contribute to cell functioning as do genes. "These sequences have the ability to copy themselves and then reinsert elsewhere in the genome," Rokhsar says. He likens them to viruses confined within a sorghum cell, not infectious but capable of replicating in much the same way viruses do. "They spread themselves throughout the genome in sort of a selfish way to help shape the structure of the genome," he explains. "In the rest of the sequence are the genes, and, at least naively speaking, we think those are what's performing the functions of the cells that make up the plant."

The corn genome blueprint is now being mapped out. Corn is a very close relative to sorghum evolutionarily speaking, separated by 10 million to 15 million years according to Paterson. He says sorghum will help to align and assemble the maize genome. What makes decoding corn's genome more difficult than sorghum's is the extra repetitive DNA found in it, and that it has experienced a duplication of its entire gene set since separating from sorghum.

The repetitive "viral-like" elements in sorghum outnumber bona fide genes by around 10 to 1, Rokhsar says. But finding actual genes within the genome is like finding a needle in a haystack. Even once genes are isolated and identified, they alone cannot tell researchers why, for instance, sorghum needs less water to thrive than other crops. The vast majority of genes in grasses like sorghum and rice are going to be put in correspondence with each other, Rokhsar says. "If sorghum has a gene it's very likely rice has a version of that same gene," he explains. "For sorghum, it's not the particular gene accounting for drought tolerance, but the gene variation that is going to be helping."

Applications of New Knowledge
Two of the most desired traits sorghum possesses are its ability to grow with relatively little moisture, and to produce good crop yields with fewer nutrient inputs such as nitrogen, which is not a trait it shares with its cousin corn. Paterson says a sorghum crop will use about half the amount of water a similar-sized corn crop would need. Like any crop, sorghum will respond to more water by producing higher yields, but according to Lust, it's not just sorghum's ability to provide good yields with less moisture that breeders admire. "From a timing standpoint it can wait two to three weeks for that moisture but for some of the other crops, the timing of that moisture is critical," Lust tells EPM. "Also, sorghum is extremely good in nitrogen use efficiency and we will get more yield with additional nitrogen, or we can utilize less nitrogen to do the same."

Sorghum's efficiency at using nitrogen and tolerance to dry weather are the result of a millennia of evolution and its domestication history in northeast Africa on marginal lands. "I think these qualities arose from the selection pressures by farmers in Africa where this crop grew up," Dahlberg says. "Are there genes associated with those qualities? There probably are, but if it was a big major gene we'd probably have already found it through classical breeding methods. It's pretty easy to find a major gene fairly quickly, but when you start talking about nitrogen use efficiency and drought tolerance, it's a lot more difficult to see that in the field—to see that incremental increase. It's going to take a lot more work to figure out those kinds of things."

Another important agricultural area where the sorghum genome might help is in weed control, according to Paterson. "Sorghum is a very close relative of Johnsongrass," he says. "Sorghum's analysis is shedding light on the nature of weediness and how we might better control it."

The sequencing of the sorghum genome is highly anticipated to have positive effects on development of modified bioenergy crops, but unless there is a surprise discovery made of a major gene that is responsible for sorghum's desirable traits, the biorefining world will still have to wait years before tangible results are employed in biomass-to-ethanol conversion. "It's more of a tool that accelerates things rather than one that gives answers right away," Rokhsar says. What may take even longer for sorghum's traits to benefit bioenergy applications, according to Dahlberg, is the lack of consensus on exactly what characteristics are most preferred in a bioenergy crop. "We really don't know quite yet what we need to be looking for in these crops," he says. "You get a whole bunch of different answers—‘I want high lignin,' or ‘I want low lignin,' or ‘I want this particular compositional makeup.' There are just a lot of different answers to that question right now and that makes it a bit more complicated. Can we work on lower lignin sorghum? Sure, we already have forage sorghums with lower lignin content. But does that translate into more efficient ethanol production? I think that's a question that still has to be answered. But the beauty behind having this kind of information available is that we'll be able to tailor plants to meet particular biorefinery needs."

Rokhsar says there are many tantalizing clues sorghum genetic researchers have to work with now that the first genome of its type has been mapped out. Gene variations that give way to improved water and nitrogen efficiency and drought stress resistance, like those scientists hope to soon identify in sorghum, are surely resident in other plant genomes. "But what is magic about the sorghum versions of those genes is something I don't think we know yet," Rokhsar says. "To understand this, we really need to know how these genes function in detail. We know it's there and we can work with it in sorghum now, but the devil is really in those variations—and that's the next step."

Ron Kotrba is an Ethanol Producer Magazine senior writer. Reach him at [email protected] or (701) 738-4942.