Soybean accounts for 70 percent of the world's edible protein and it is hoped that the research will help advance new breeding strategies.
Soy protein is used in the food industry as a low-fat source of protein but risks to the crop, such as water mold which causes stem and root rot, can affect supply and soybean prices have soared over the past year, nearly doubling in price.
Scientists hope the knowledge gained on the genetic makeup of soy could be used to reduce the risks to crop supplies.
Jeremy Schmutz of the US Department of Energy Joint Genome Institute (DOE JGI), said: "We have ordered and localized about 5,500 genetic markers on the sequence, which promise to be of particular importance to those researchers seeking to optimize certain qualities in soybean."
A genetic marker represents a known location on a chromosome that can be associated with a particular gene or trait.
Prospective genome pathways of interest are those that directly influence yield, oil and protein content, as well as drought tolerance and resistance to nematodes and diseases.
USDA chief scientist and under secretary for research, education, and economics Dr Gale Buchanan, said: "Soybeans have been an important food plant providing essential protein to people for hundreds of years.
"Now, with the new knowledge available through this joint DOE/USDA genome sequencing project, researchers everywhere will be able to further enhance important traits that make the soybean such a valuable plant."
Biofuel
According to 2007 US census data, soybean is estimated to be responsible for more than 80 percent of biodiesel production.
DOE JGI's interest in sequencing the soybean centers on its use for biodiesel.
DOE under secretary for science Dr Raymond Orbach, said: “The genome sequence is the direct result of a memorandum of understanding between DOE and USDA (US Department of Agriculture) to increase interagency collaboration in plant genomics.
"We are proud to support this major scientific breakthrough that will not only advance our knowledge of a key agricultural commodity but also lead to new insights into biodiesel production."