Comprehensive silk gland multi-omics comparison illuminates two alternative mechanisms in silkworm heterosis
摘要: 杂种优势是动物和植物中的普遍存在的一种现象，其潜在机制复杂多样。该研究以两种常用的家蚕杂交系统为模型，利用多组学技术,以回答两个问题：不同杂交策略之间是否存在可能的内在关联；表观遗传机制对家蚕杂种优势的贡献。我们证明了两个杂交系统之间的丝腺转录组格局存在显著差异，表现在杂交优势后代与亲本相比的基因表达水平差异和表达模式差异。四元杂交系统的杂交优势主要是由上调基因和亲本显性上调表达模式基因引起，这些基因主要参与多种转运过程、细胞氮化合物分解代谢、葡萄糖代谢过程以及三羧酸循环（TCA循环）。与此相反，二元系统的杂种优势则是由下调基因和超亲下调表达模式基因引起，这些基因主要参与机体基本的氮合成代谢和运作。该研究还证明了 DNA 甲基化可以通过调节一些杂种优势相关基因的表达来促进杂种优势。总的来说，我们阐明了两种可能有助于蚕杂种优势形成的备选机制，这两种机制都是有利于提高能源和氮的利用效率来提高蚕丝产量。Abstract: Heterosis is a common phenomenon in plants and animals with diverse underlying mechanisms. Here, we applied two widely used silkworm hybrid systems and performed multi-omics analysis to identify possible intrinsic associations between different hybrid strategies and epigenetic mechanisms with silkworm heterosis. We found significant differences in the silk gland transcriptomic landscape between the two systems, including differentially expressed genes and expression patterns in the hybrid offspring compared to their parents. In the quaternary hybrid system, hybrid vigor was primarily due to up-regulated genes and the parent-dominant up-regulated expression pattern, involving multiple transport processes, cellular nitrogen compound catabolism, glucose metabolism, and tricarboxylic acid cycle. In the binary system, hybrid vigor was mainly due to the down-regulated genes and transgressively down-regulated expression pattern, mainly involving basic nitrogen synthesis metabolism and body function. We also demonstrated that DNA methylation may affect hybrid vigor by regulating the expression of several heterosis-related genes. Thus, this study revealed two alternative mechanisms that may contribute to silkworm heterosis, both of which facilitate the efficient utilization of energy and nitrogen for silk production.
Figure 1. Offspring of two hybrid systems showed significant hybrid vigor
A: Design of quaternary and binary hybrid systems. B, C: Statistical results of phenotypes of total cocoon weight and cocoon shell weight for quaternary hybrid system. D, E: Statistical results of phenotypes of total cocoon weight and cocoon shell weight for binary hybrid system. Significant differences are indicated as *: P<0.05, **: P<0.01, and ***: P<0.001, two-tailed t-test. F: PCA based on genome-wide SNP data of both systems. G: PCA based on gene expression data of both systems.
Figure 2. Comparisons of DEGs between hybrid offspring and their parents in two hybrid systems
A, B: Classification of up-regulated (A) and down-regulated (B) DEGs between seven groups in quaternary hybrid system. C, D: Classification of up-regulated (C) and down-regulated (D) expression genes between four groups in binary hybrid system. E, F: Overlapping up-regulated (E) and down-regulated (F) DEGs between two groups (F1_vs_F2 in quaternary system and F0_vs_F1 in binary system). G: Enrichment analysis of up-regulated DEGs in E. H: Enrichment analysis of down-regulated DEGs in F. Black text indicates GO term and blue text indicates KEGG pathway in G and H.
Figure 3. Differences in DEPGs between two hybrid systems
A: Distribution of DEPGs in hybrid offspring in quaternary hybrid system. B: Functions of PDU genes in hybrid offspring in quaternary hybrid system. C: Distribution of DEPGs in hybrid offspring in binary hybrid system. D: Functions of TD genes in hybrid offspring in binary hybrid system. E: Overlapping MDD genes in hybrid offspring between hybrid systems. F: Functions of MDD genes in hybrid offspring in binary hybrid system. Black text indicates GO term and blue text indicates KEGG pathway in B, D and F.
Figure 4. Contribution of DNA methylation to hybrid vigor formation
A: PCA based on genome-wide SNP data of quaternary hybrid system. B: PCA based on gene expression data of quaternary hybrid system. C: PCA based on methylation level of gene body region of quaternary hybrid system. D: Classification of genes with DMRs in gene body region among seven groups in quaternary hybrid system. E: Classification of genes with DMRs in promoter region among seven groups in quaternary hybrid system. F: Overlapping genes with DMRs in gene body region between different varieties (JF0_vs_CF0 and JF1_vs_CF1) or between hybrid individuals and parents in quaternary hybrid system (F1_vs_F2).
Figure 5. Two PDU genes involved in protein synthesis and transport are regulated by DNA methylation
A: Overlapping PDU genes and genes with DMRs in gene body region between hybrid offspring and their maternal parent in quaternary hybrid system. B: Methylation level and read depth of DMR in twelfth intron of GLEAN_00865 gene in hybrid individuals and their parents. C: Methylation level and read depth of DMR in seventh exon of GLEAN_05534 gene in hybrid individuals and their parents. D: Methylation level of DMRs and expression level of GLEAN_00865 and GLEAN_05534 genes in hybrid individuals and their parents.
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