Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany.
National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
Theor Appl Genet. 2023 Apr 18;136(5):113. doi: 10.1007/s00122-023-04345-7.
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. 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 F hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.
在种子和幼苗发育过程中对基因表达和小 RNA 进行转录组和表观基因组分析，揭示了杂种优势早期表达的表达和甲基化优势水平，对油菜具有重要意义。杂种通过杂种优势提高性能仍然是植物育种的一个关键方面；然而，其潜在机制仍未完全阐明。为了研究转录组和表观基因组模式在杂种优势早期表达中的潜在作用，我们使用下一代测序技术研究了来自两个不同甘蓝型油菜生态型的杂种在种子和幼苗发育阶段的基因表达、小 RNA 丰度和全基因组甲基化。总共鉴定了 31117、344、36229 和 7399 个差异表达基因、microRNAs、小干扰 RNA 和差异甲基化区域。大约 70%的差异表达或甲基化特征表现出亲本优势水平，杂种遵循与亲本相同的模式。通过种子发育过程中的基因本体富集和 microRNA-靶标关联分析，我们发现了具有超亲性和父本优势模式的生殖、发育和减数分裂基因的副本。有趣的是，在种子形成过程中，母本优势在高甲基化和下调特征中更为明显，与被子植物配子发生过程中普遍报道的母本配子去甲基化形成对比。甲基化与基因表达之间的关联允许鉴定在种子形成过程中具有多种关键生物学功能的假定表观等位基因。此外，大多数差异甲基化区域、差异表达的 siRNAs 和转座元件位于没有差异表达的基因侧翼区域。这表明，在杂种背景下，表观基因组特征的差异表达和甲基化可能有助于维持关键基因的表达。F 杂种在种子形成过程中的差异表达和甲基化模式为早期杂种优势中具有潜在作用的基因和机制提供了新的见解。
