Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species.

A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may confer an advantage in populations with small effective size. However, contradictory evidence for the correlation with environmental variation, and limited understanding of the underlying genetic mechanisms, has cast doubts on the adaptive role of genome size variation. To address this, we studied two Hordeum species which were collected at the same sites along a wide range of environments but differ in life habits (annual/perennial) and mating strategy (self/outcrossing). We detected substantial genome size variation, with differences of up to 10% in both species. While the mating system influenced the distribution of variation within populations, it did not alter the overall range of genome sizes. Drought emerged as the primary environmental factor associated with larger genomes, with past transposable elements (TE) bursts identified as the potential source of genome expansion. Genome-wide association analyses revealed that TE silencing is central to genome size regulation, with selection maintaining smaller genomes among individuals with higher fitness in favorable habitats. Under stressful conditions, silencing becomes less efficient, allowing larger genomes to persist and thereby increasing the reservoir of genetic variation available for selection. Together, these findings provide an integrative view of genome size dynamics in natural populations and underscore its exaptive role in maintenance of genetic variation under environmental stress.