Extending the genotype in Brachypodium by including DNA methylation reveals a joint contribution with genetics on adaptive traits

Epigenetic changes have been considered a potential missing link underlying phenotypic variation in selectable traits but is confounded with substantial genetic variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenetic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, the reduced genetic diversity also resulted in diminished variation in DNA methylation within families. Mixed-effects linear modelling revealed large genetic differences between families and a minor contribution of epigenetic variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation towards heritable phenotypic variation relative to genetic differences.