A Genome-Wide Comparison of Structural Variation Following Mutagenesis, Genetic Transformation and Tissue Culture Treatments in Soybean

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 germplasm: inter-varietal, fast neutron mutants, and plants that have experienced a 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 indicates that this type of variation is essentially inconsequential to products developed from a trait introgression pipeline.