Genotyping of the more than 19,000 soybean accessions in the USDA Soybean Germplasm Collection will enable soybean breeders to develop and select seeds for better disease and insect resistance and other traits that are needed for specific field and climate conditions, according to a USDA researcher.
Perry Cregan, PhD, a research leader at the Soybean Genomics and Improvement Lab of the USDA’s Agricultural Research Service in Beltsville, Md., says that researchers there have successfully genotyped the USDA’s entire cache of more than 19,000 soybeans, both cultivated and wild types, that have been collected from all over the world.
Dr. Cregan and coworkers developed a beadchip containing more 50,000 single nucleotide polymorphism (SNP) DNA markers, providing genetic information that will allow seed companies and researchers at state universities and the USDA to work with and select from the wide genetic variability present in this large collection of soybean types, he says. The development of the tool was reported last year in PLOS One.
Since that publication, the researchers have analyzed the whole USDA germplasm collection and selected 5,400 markers that were spread evenly across the 20 soybean chromosomes.
“This is the raw material that [seed companies and researchers] need, the analysis of the whole germplasm collection,” Dr. Cregan says. “Those DNA markers were selected to be the most informative, and they are already being used in the new beadchip,” by soybean geneticists and breeders for the discovery of genes controlling traits of interest.
With access to the database, “soybean breeders can analyze these soybeans for traits that they are interested in. By using genetic association analysis, they can find the position in the genome where the genes that control these traits are located. They can then use specific genetic markers to incorporate these naturally occurring genes from different soybean accessions into their cultivated varieties to improve their disease resistance, seed quality, drought resistance, or protein levels,” Dr. Cregan tells Food Quality & Safety in an interview.
The SNP information available through the work of this project allows researchers and soybean breeders to cross genotypes and look for progeny that have the desirable traits. “You would cross your high-yielding soybean that you grow all the time in the field with the source of resistance, and then you would look for progeny that carry the resistance. That’s why you use the markers: You want to get just that piece of DNA from the source that carries the gene or genes for resistance, maintaining everything else for the good genotype that you have,” he says.