Genome Editing in Flax in Response to Stress

The flax genome can be rapidly modified within a single generation in response to the growth environment. The variations do not appear to be due to either random mutations or the movement of transposable elements, but rather that the genome appears to be able to switch between two well-defined, different sequences at many loci. The genomes of 9 lines, the progenitor line (Pl) and 8 derived lines (genotrophs) have been compared, by whole genome sequencing, using the flax variety Bethune as the reference genome. The identified differences fall into two main classes. One, where regions of the genome have insertions or deletions (indels) among the genotrophs compared to Pl, the second where Pl and the genotrophs have a large number of SNPs over a short region of the genome. Subsets of these indel variants have been assayed in the progeny from 19 individuals from three different nutrient regimes, from other flax accessions and even the wild progenitor of flax, Linum bienne, have been characterized. In every case the same two alternative structures are seen. What is the source of these variants since they are not present in an intact form in the progenitor genome? Such reproducible large scale variation is unlikely to occur through multiple independent events and therefore an editing mechanism by which long tracts of the genome can be replaced with an alternative structure has been proposed.