1a. Objectives (from AD-416):
Compare the genomic changes that have occurred with 70 years of selection in the commercially used pool of soybean breeding in the U.S. with the genomic changes that have occurred with 30 years of selection in an alternative gene pool that we have created from exotic germplasm given that yield of the final products in both system are equal.
1b. Approach (from AD-416):
We will determine the genetic relatedness of the 35 major ancestors of U.S. soybean varieties and the 54 exotic accessions that we have successfully used as parents, using the nearly 50,000 SNP markers currently characterized on all of the annual accessions in the USDA Soybean Germplasm Collection. With these data, we can estimate the degree of genetic relatedness among these lines, identify significant differences between the two sets of lines, and use the genotype data from these ancestors to identify the origin of regions that appear to be selected for in lines developed from these two gene pools. We will track the regions of the genome that have been changed or retained through 7 decades of U.S. soybean breeding using the 35 major ancestral lines, the 524 publicly released varieties and the 53 privately developed varieties that are in the USDA Soybean Germplasm Collection. Those regions that are consistently retained in multiple varieties derived from a single ancestor line are likely to be the regions under selection by plant breeders in the process of increasing yield. We will also determine the regional effects on genetic selection by comparing genomic changes in varieties in three different maturity ranges (maturity group 00 to I, II to IV and V to VIII). Because growing conditions vary greatly between northern Minnesota and southern Georgia, it is very likely that the genes that are important in producing high yield may not be the same in all areas. We will determine the genomic changes that have occurred within our breeding program by tracking the regions of the genome that have been changed or retained through 3 decades of selection using the 54 exotic accessions that we have successfully used as parents and the 141 experimental lines that we have developed from these exotic accessions. These experimental lines are either high yielding lines or intermediate lines that were derived from exotic germplasm and are in the pedigrees of our highest yielding lines. Using these intermediate lines, will help us determine which genomic regions were selected in the process of increasing yield in our breeding program. Finally we will determine if there are important genomic change differences between the varieties developed in commercial breeding programs and the lines derived from exotic germplasm in our breeding program. Those regions that are consistent between the two groups are likely to be areas of global importance to yield and would be the focus of future research to determine the specific genes that may be affecting yield in those regions. Those areas that are consistent within groups but different between groups will indicate important genetic differences between the two gene pools. These regions are perhaps the most valuable potential discovery as they could be combined in future varieties using genomic selection to enhance yield. Our goal is to identify genomic regions that are associated with increased yield for which the lines derived from exotic germplasm are different from our commercial varieties.
3. Progress Report:
The project to characterize all of the annual accessions in the USDA Soybean Germplasm Collection with approximately 50,000 DNA markers (Single nucleotide polymorphisms, SNPs) will be completed this summer. We will use these data for all of the ancestors of current U.S. varieties as well as all of the exotic accessions used in our breeding program to estimate the degree of genetic relatedness among these lines, and identify significant differences between the two sets of lines. We planted 130 experimental lines that represent our highest yielding experimental lines and the experimental lines in the pedigrees of these lines. We also planted 65 lines of our most recently developed lines in multiple location yield tests to collect another year of yield data. From the data collected on these lines, we will select approximately 20 additional high yielding lines to add to our set of experimental lines that will be characterized with the 50,000 SNP Illumina iSelect Genechips. The addition of these lines will allow us to track changes through as many as four cycles of selection.