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Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Allopolyploids also exhibit homoeologous exchange that recombines, duplicate, or delete homoeologous regions of the newly formed genome. These kinds of changes to gene dosage are hypothesized to be constrained by selection to maintai...
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... direction of dosage changes and proportion of regions with changed dosage varied greatly between lines and generations with no consistent pattern significantly favoring the BnA or BnC subgenome (Fig 3a). Individual lines ranged in the number of exchanged homoeolog pairs from 114 to 10,231 (Table 1).Overall, nine of 18 plants had significantly more genomic . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. ...Similar publications
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... The extent of these features in an allopolyploid model crop like B. napus also have potential implications in other polyploid crops where heterosis still remains to be exploited, such as wheat and potatoes (Steeg et al. 2022). Patterns of expression and methylation dominance levels could also contribute a new level of understand regarding allele-specific gene expression (Fan et al. 2020;Sands et al. 2021), isoform expression (Vitting-Seerup and Sandelin 2019; Yao et al. 2020;Golicz et al. 2021), gene fusion and dosage (Mahmoud et al. 2019;Serin Harmanci et al. 2020;Bird et al. 2021b) as well as non-germline omics variations among F 1 plants and populations (Higgins et al. 2018;Cortijo et al. 2019;Orantes-Bonilla et al. 2022;Quezada-Martinez et al. 2022). Their role in heterotic gene expression patterns is ultimately also of interest for transcriptome-based genomic selection or hybrid performance prediction (e.g. ...
Key message
Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape.
Abstract
The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.
