Widespread genome instability in Solanum tuberosum plants regenerated from protoplasts

Abstract

Non-transgenic genome editing in regenerable protoplasts, cell-wall free plant cells, could revolutionize crop improvement because it reduces regulatory and technical complexity. But, plant tissue culture is known to engender frequent unwanted variation. To evaluate the contribution of genome instability to this phenomenon, we analyzed large scale copy number changes in potatoes regenerated from protoplasts by comparison of Illumina read depth. While a control set of plants that had been propagated by cuttings displayed no changes, the protoplast regenerants were affected by pervasive aneuploidy. In addition, certain chromosomes displayed segmental deletions and duplications ranging from one to many. Resampling the same plant found different dosage profiles in different leaves, indicating frequent persistence of instability.