The scientists say that the two lines will be given away to breeders seeking to produce new varieties of allergy-free soybeans without genetic engineering.
The breakthrough could help food makers tap the growing free-from food market, which is set to double on the back of growing consumer concern over health and well-being.
Market analyst Mintel says that the UK sector, which is being driven by increased public awareness of food allergies and intolerance, has already enjoyed sales growth of over 300 per cent since 2000.
In addition, because the newly identified lines occur naturally, they can be successfully crossed into other soybean lines "without any biotechnology-derived component," the researchers noted.
Crop scientists at the University of Illinois at Urbana-Champaign and the USDA-Agricultural Research Service's Donald Danforth Plant Science Centre in St. Louis screened more than 16,000 soybean lines kept in the USDA's National Soybean Germplasm Collection.
It was discovered that two soybean lines (PI 567476 and PI 603570A) contained virtually identical genetic mutations that do not contain the leading allergy-causing P34 protein, which consists of 379 amino acids.
"We are releasing this information with no patents so that companies and breeders involved with soybeans can incorporate these two lines as quickly as possible," said Theodore Hymowitz, emeritus professor of plant genetics in the crop sciences department at the University of Illinois.
Companies in Japan, Canada and across the United States have been following the research effort, he added.
The research, which was funded primarily by the Illinois-Missouri Biotechnology Alliance, went through two stages.
First, using a specially developed immunochemistry approach, Hymowitz's post-doctoral assistant Leina M. Joseph examined 100 lines of soybeans per day for nine months from the UI-based collection. Seeds were crushed, treated and placed on a membrane for screening.
A second screening using stronger antibodies and protein gels was done to confirm the absence of P34 in the two domestic lines.
After the two lines were isolated, seeds were sent to the Danforth Centre for additional molecular analysis to determine why P34 was absent. Six identical genetic mutations were found in each, indicating the two lines may be related.
"The lack of the protein was confirmed by more-detailed two-dimensional protein assays," said Eliot M. Herman, a lead scientist at Danforth who probed the seeds with post-doctoral researcher Monica A. Schmidt.
"We then isolated the gene responsible for the lesion, and we found there was a single significant change in the gene's sequence that likely produced a protein which could not be made as a stable product."
Herman discovered P34 in the early 1990s and in 2003 had successfully used a gene-silencing technique to create a soybean line in which P34 was 'knocked out.' However, because of public resistance to genetically modified products researchers have been seeking a more traditional approach.
The findings will appear later this year in the journal Crop Science.