Comparison of Genomic Structural Variation Associated with Cultivars, Mutagenized, and Transgenic Soybean Plants

Plant genetic transformation and tissue culture is an important component of modern plant breeding. In addition to the introgression of a desired transgene, somaclonal variation is a well-established side effect of the plant tissue culture process. We used a comparative genome hybridization array to compare genic structural variation in three different classes of soybean germplasm: inter-varietal, fast neutron mutants, and plants that have experienced an Agrobacterium-based genetic transformation and tissue culture (GTTC) process.  In the five GTTC genotypes studied, only two confirmed large deletions were associated with the GTTC process.  The frequency of these events is approximately one order of magnitude less than that observed following fast neutron mutagenesis and two orders of magnitude less than standing inter-varietal structural variation.  This comparison provides a fresh perspective on the relative rates of genomic variation associated with these germplasm sources.  The rarity of structural variants following GTTC plus the common practice of extensive backcrossing following transformation suggests that this type of variation has minimal impacts on the products developed from a trait introgression pipeline.