Abstract
BackgroundPolyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown.ResultsWe probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity.ConclusionsThe present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.
Highlights
Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding
Following the default read-filtering step, we obtained 797.6 million pairs of highconfidence Hi-C reads
A similar two diagonal pattern was reported for barley [27] and reflects the Rabl configuration [28], in which chromosomes fold back with centromeres and telomeres clustering at the opposite sides of the nucleus, leading to the adjacency of long and short arms
Summary
Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. The mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. Its three subgenomes, which form an extremely large genome (16 Gb) comprising long chromosomes (499–869 Mb), raise a series of interesting questions regarding higherorder chromatin organization and the underlying mechanism. Common wheat is a relatively young hexaploid species that evolved via two polyploidization events [1, 2], the first of which involved a hybridization between the diploid wheat species Triticum urartu (AA, 2n = 2x = 14) and an unidentified Aegilops species. Interactions are more common between subgenomes A and B than between subgenomes A and D or B and D These findings indicate that the higher-order chromosomal organization may be maintained following tetraploidization and hexaploidization processes [3]. The molecular mechanisms associated with these specific subgenome regions remain largely unknown
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