Introducing new genetic variation from DD genome progenitors of hexaploid wheat into breeding programmes is a key part of wheat improvement due to the relatively narrow base of DD genome variation in current breeding populations. The addition of a large, closely related DD genome to a tetraploid AABB genome to form a stable hexaploid AABBDD genome provides an interesting opportunity to analyze epigenetic states and interactions of homoeologous genes and repeats in their diploid, tetraploid and hexaploid contexts.

We show that gene expression, DNA methylation, chromatin accessibility and interactions, and histone modifications are highly dynamic in newly formed hexaploid lines, with the DD genome undergoing higher levels of changes than the AA and BB genomes.

We are establishing how these changes may lead to stable gene regulatory and expression patterns. In the case of dominant, suppressed and balanced triad formation in leaf, developing grain and meiotic tissues, new expression patterns are rapidly established, many of which mirror in part those seen in stable hexaploids, with meiotic patterns being the most conserved at each ploidy level and grain development the most dynamic.

Gene methylation had a very minor influence on gene expression changes. Some regulatory networks during grain development have the same overall topology at each ploidy level but expand to incorporate new genes. Other storage protein networks incorporate DD genome transcription factors into a more dominant control of gluten genes, while some networks remain independent and are unaffected by ploidy changes.

Repeated elements, specifically the abundant and well-annotated full-length LTR classes, show decreased methylation, increased expression and chromatin accessibility as they age. Only a few young fl-LTR elements exhibited high expression levels of full-length transcripts, indicating potential transpositional activity.

Approximately 9 elements were differentially expressed upon hexaploid formation, and only three of these were associated with loss of DNA methylation, indicating that LTR elements appear to be mainly quiescent during wheat synthetic formation.

This suggests that epigenomic and genomic interactions are the primary mechanisms integrating the activities of newly formed hexaploid wheat genomes.