Flax Genome “Edits” in Response to the Growth Environment

Abstract

The flax genome can be rapidly modified within a single generation in response to the growth environment. The variations that occur do not appear to be due just 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 nine lines, the progenitor line (Pl) and eight 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 and 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 3 different nutrient regimes, from other flax accessions and the wild progenitor of flax, Linum bienne. In every case the same two alternative structures were seen. The source of these variants, since they are not present in an intact form in the progenitor genome, is intriguing. 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.