The transposable elements syndrome of wheat domestication

Domestication marks a turning point in human history, driving substantial genomic modifications in cultivated plants. Tetraploid wheat was one of the Neolithic founder crops and remains a major cultivated species today. We investigated how domestication altered the abundance and distribution of transposable elements (TEs) and structural variation (SV) in wheat, revealing genomic changes associated with key domestication traits. Our results demonstrate that extensive TE proliferation before and during the Pleistocene–Holocene transition expanded standing genetic variation and phenotypic diversity. This expansion has provided the raw material for selection by the early farmers including a Gypsy insertion in the BTR1 -3B gene causing a loss of function and contributing to the establishment of the non-shattering phenotype. We further show that purifying selection was more efficient in purging TEs among wild populations, whereas domesticated wheat has maintained TE clusters around genes that are under selection. We propose a model in which climatic instability triggered genome-wide TE bursts, expanding genetic variation including at domestication traits. As climate stabilized, purifying selection gradually removed deleterious TEs insertions, while early farmers selectively preserved advantageous phenotypes, thus maintaining TE-rich regions around key domestication genes. This model provides an integrative framework linking climate driven genomic changes, selection, divergence and domestication.