Mauricio Orantes-Bonilla, Hao Wang, Huey Tyng Lee, Agnieszka A. Golicz, Dandan Hu, Wenwen Li, Jun Zou & Rod J. Snowdon

Theoretical and Applied Genetics May 2023; vol. 136, Article number: 113

Published: 18 April 2023

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.

See https://link.springer.com/article/10.1007/s00122-023-04345-7

Figure 2: Percentages of differentially expressed genes (DEGs), differentially expressed miRNAs (DE-miRNAS), differentially expressed siRNAs (DE-siRNAS) and differentially methylated regions (DMRs) in CpG and CHG methylation contexts by expression level dominance (ELD) and methylation level dominance (MLD) patterns per stage. Increase and decrease in expression and methylation per patterrn are displayed by the dot-ended lines showing the relative expression or methylation levels for the parental genotypes Express 617 (E) and G3D001 (G) along with their F₁ hybrid (F). Differential expression and methylation are displayed for leaf samples at stage BBCH16 and for ovules at 15 (OS15) and 30 (OS30) days after pollination by selfing (F₁ ovules) or cross-pollination between the two parental lines (F₀ ovules). Percentages are displayed with colored backgrounds to represent high (red) or low (blue) abundance