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Abstract Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
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This content will become publicly available on September 15, 2025
Homoploid Hybridization Resolves the Origin of Octoploid Strawberries
Abstract The identity of the diploid progenitors of octoploid cultivated strawberry (Fragaria × ananassa) has been subject to much debate. Past work identified four subgenomes and consistent evidence forF. californica(previously namedF. vescasubsp.bracteata) andF. iinumaeas donors for subgenomes A and B, respectively, with conflicting results for the origins of subgenomes C and D. Here, reticulate phylogeny and admixture analysis support hybridization betweenF. viridisandF. vescain the ancestry of subgenome A, and betweenF. nipponicaandF. iinumaein the ancestry of subgenome B. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports ofF. viridisandF. nipponicaas donors of the C and D subgenomes and unify conflicting hypotheses about the evolutionary origin of octoploidFragaria.
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- Award ID(s):
- 1912180
- PAR ID:
- 10579859
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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