To understand a complex subject, sometimes it’s more prudent to look to its smaller segments first.

Well, a genome is defined as the total genetic content contained in an organism—its DNA and the nucleotide bases fragments that make it up. Genome sequencing is one of the latest techniques used by researchers in studying the mysteries of various organisms.

“Genome sequencing is the determination of the entire set of hereditary instructions for an organism,” said Andrew Paterson, director of the Plant Genome Mapping Laboratory at the University of Georgia, in Athens and lead project researcher. “For sorghum, it will be carried out by breaking the entire genome into small overlapping fragments, determining the arrangement of the four letters in the DNA alphabet for each fragment, then using the overlaps among the fragments to stitch them together.” The building blocks of DNA are four basic chemical units: Adenine (A), guanine (G), cytosine (C) and thymine (T). When these letters combine into the base pairs of AT, TA, GC and CG they form the rungs of the double helix of DNA.

Researchers will sequence the genome to learn what it encodes so that they can better understand the plant’s life cycle and the genetic basis of important plant traits such as drought tolerance. The process is called “whole-genome shotgun sequencing,” according to the JGI project website. Researchers randomly shear a representative sample of an organism’s DNA through a specific process, sequence multiple fragments of the DNA with overlapping sequences and then infer the original sequence by reassembling the fragments.

“Essentially, sorghum DNA will be sent to the Joint Genome Institute (JGI), the Department of Energy’s genome sequencing center, where the DNA will be shotgun sequenced,” said John Mullet director of the Institute for Plant Genomics and Biotechnology at Texas A&M University, College Station. “By this I mean randomly sequencing small blocks of DNA for subsequent assembly into continuous sequence to the extent possible. A first stage assembly of the shotgun sequence will be released into the public domain by about December 2006, at which time the sorghum research community will follow up with further sequencing, assembly, and annotation for genes, etc.”

Why sequence the sorghum genome?

The first step in this lengthy process was getting the sorghum plant accepted into the Department of Energy’s genome sequencing program.

Jeff Dahlberg, research director for the National Sorghum Producers, explained that it was a series of fortunate events that lead to sorghum’s sequencing.

The DOE put out a request for proposals to the scientific community at large for genomes to be selected for sequencing. A proposal for the sorghum genome was created by Paterson, with the help of NSP and other partner organizations, and accepted from among the many proposals that year.

One reason sorghum was accepted as a project is its close relation to rice, a crop already sequenced, and corn, which has yet to be fully sequenced.

“Sorghum is the stepping stone between rice and corn,” Dahlberg said. “By sequencing sorghum, it will help in gene discovery in crops like corn and rice that have similar genes.” Also, genetic engineers may find genes similar in the sorghum crop that they can add to rice or corn for more desirable traits.

“We’re hoping to obviously find additional drought tolerance,” Dahlberg said. “We hope to use the genome to help find genes that regulate drought tolerance and control it. It’s a question of how do we make the most efficient use of water for higher yields? By understanding the genes and how they interact, in the future we may be able to manipulate them to express at proper times and keep yields high under stressful situations. The same argument goes for disease and insect resistance too.” The harder part, he said, will be finding out where the sequencing will lead researchers. Various combinations of genes and what they turn on and off in the plant, how they regulate how the plant interacts with the environment, these sort of questions will take longer to answer, Dahlberg added.

“This work will reveal the entire genetic potential of the sorghum genome, revealing potential weaknesses that we can remedy by incorporation of genes from other crops, and identifying valuable functions such as its ability to withstand drought that would be of value to transfer to other crops,” Paterson added.

According to the project’s website, www.jgi.doe.gov/sequencing/why/CSP2006/sorghum.html, sorghum is also an important crop to sequence because it is a model for tropical grasses, such as rice, the first monocot plant to be sequenced. “Sorghum is representative of the tropical grasses in that it has ‘C4’ photosynthesis, using a complex combination of biochemical and morphological specialization’s resulting in more efficient carbon assimilation at high temperatures. By contrast, rice is more representative of temperate grasses, using ‘C3’ photosynthesis,” according to the JGI site. Tropical grasses have a worldwide collective minimum economic impact of $69 billion each year.

Additionally, sorghum can be a reference tool for work on assembling and analyzing the maize genome, which is four times the size of sorghum. Sorghum is also a close relative of sugarcane, which produces about 140 million metric tons for a net value of about $30 billion each year.

“Sorghum and sugarcane are thought to have shared a common ancestor about 5 million years ago,” according to the JGI site. “The two have retained largely common gene order, and some genotypes can still be intercrossed.”

“Sorghum and its ‘kissing cousin,’ sugarcane, are among the world’s most efficient biomass producers, and are among the leading biofuels crops,” Paterson said. “Worldwide energy needs are likely to depend to a growing degree on biofuels. The sequence will increase researchers’ knowledge of the sorghum genome and accelerate our progress at developing new genotypes that are optimized for biomass production (or grain production).”

And, the Sorghum genus is noteworthy in that it includes the noxious weed Johnson grass (Sorghum halepense). The same features that make Johnson grass so annoying to producers are actually desirable in many more genetically complex forages, turfs and biomass crops. So, in a way, by sequencing sorghum, researchers might find answers to weed biology questions.

“While it will be many years before we understand the exact relationship between each gene and its function, we will have a growing ability to rapidly respond to new challenges that face producers, processors, and consumers, with intrinsic low-cost genetic solutions,” Paterson said. “We also expect the sorghum genome to reveal new clues as to the identities of the specific genes that were responsible for cereal domestication, one of mankind’s greatest achievements in that efficient cultivation permitted the dramatic expansion of human populations.”

What is the status of the project today?

Sequencing itself is already underway and should be completed in mid- to late-2006, Paterson said. “However it will take perhaps another year to produce an initial assembly of the sequence (stitching the pieces together), and an early annotation, which will begin to determine the number of genes in sorghum and describe their possible roles,” Paterson added.

“The sequencing of the sorghum genome is the culmination of 15 years of work that began with making a genetic map, with DNA landmarks to identify particular locations in the genome,” Paterson said. “The genetic map led to the construction of a physical map, which enabled us to have in hand any segment of DNA in the sorghum genome. Because each letter in the sorghum genetic code will be sequenced an average of eight times, we can be statistically very confident that virtually all of them will be sequenced at least once,” Paterson said.

A challenge to the project, according to Paterson, is that the sorghum genome will be the largest plant genome sequenced and because of that there will be some repetitive “junk DNA” families found that can complicate the sequence assembly. However, he’s confident that the genetic and physical maps he and his lab have produced for its assembly—with significant contributions from colleagues at the Arizona Genomics Institute, Cornell University and Texas A&M University—will mitigate the problem.

Mullet explained that the map is used as a framework for the sequence to be assembled upon and it allows researchers to understand the architecture of sorghum chromosomes, such as their size, organization and distribution of genes. This framework also will allow researchers to explore the diversity of sorghum germplasm and understand the regulation of its gene expression, he said.

“Experience with other whole genome shotgun sequencing projects shows that there will be considerable additional work needed to assemble and finish a high quality sorghum genome sequence after the 8X shotgun sequence generated by DOE is released,” Mullet said.

The cost of the sequencing itself, estimated at about $5 million, will be absorbed by the U.S. Department of Energy Joint Genome Institute. Prior investments totaling about $10 million from the U.S. National Science Foundation, the U.S. Department of Agriculture National Research Initiative, the International Consortium for Sugarcane Biotechnology, and the National Grain Sorghum Producers have made this work possible, according to Paterson.

Jennifer M. Latzke can be reached by phone at 620-227-1807, or by e-mail at jlatzke@hpj.com.