Transgenerational Inheritance in Flax – Epigenetics or Structured Genome Rearrangements

Certain varieties of flax (Linum usitatissimum) respond to the growth environment with the appearance of phenotypic variation that can be inherited through many generations. At the phenomenological level these observations could be easily interpreted as epigenetic changes. However, many DNA sequence variations also arise reproducibly when these phenotypic variants are induced. The characterization of the genomes, by a variety of methods including next generation whole genome shotgun sequencing has been undertaken. A comparison of the genomes of these induced plants, their progenitor line, a cultivar and Linum bienne (the species from which flax was domesticated), has identified regions that are absent intact in the progenitor genome but reproducibly present in the induced lines and in other flax, linseed and L. bienne. Of particular interest is that when these regions are characterized in many varieties or L. bienne, the same fragments are identified, that is there seem to be alternative alleles of some regions that can be reconstructed reproducibly. The genome comparisons subdivide the flax genome into two compartments, one of which is relatively stable and the other, which is rapidly modified. However these regions are not randomly modified but changed in a programmed manner to give specific variants.  These data indicate a novel genome restructuring process that has not been previously described and can influence the interpretation of comparative genomics data.