Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 35 Qinghua East Road, Beijing, China.
New Phytol. 2020 Feb;225(3):1218-1233. doi: 10.1111/nph.16220. Epub 2019 Nov 1.
Increasing evidence indicates that DNA methylation is heritable and serves as an essential marker contributing to phenotypic variation. Linkage-linkage disequilibrium mapping was used to decipher the epigenetic architecture underlying nine growth and wood property traits in a linkage population (550 F progeny) and a natural population (435 unrelated individuals) of Populus using methylation-sensitive amplification polymorphism (MSAP)-based analysis. The interactions between genetic and epigenetic variants in the causative genes was further unveiled using expression quantitative trait methylation (eQTM) and nucleotide (eQTN) mapping strategies. A total of 163 epigenetic quantitative trait loci (epiQTLs; LOD ≥ 3.0), explaining 1.7-44.5% of phenotypic variations, were mapped to a high-resolution epigenetic map with 19 linkage groups, which was supported by the significant MSAP associations (P < 0.001) in the two populations. There were 23 causal genes involved in growth regulation and wood formation, whose markers were located in epiQTLs and associated with the same traits in both populations. Further eQTN and eQTM mapping showed that causal genetic and epigenetic variants within the 23 candidate genes may interact more in trans in gene expression and phenotype. The present study provides strategies for investigating epigenetic architecture and the interaction between genetic and epigenetic variants modulating complex traits in forest trees.
越来越多的证据表明，DNA 甲基化是可遗传的，并且作为一个重要的标记，有助于表型变异。本研究利用连锁-连锁不平衡作图，基于甲基化敏感扩增多态性（MSAP）分析，在一个连锁群体（550 个 F 代）和一个自然群体（435 个无关个体）中，对 9 个生长和木材特性性状的表观遗传结构进行了解析。通过表达数量性状甲基化（eQTM）和核苷酸（eQTN）作图策略，进一步揭示了遗传和表观遗传变异在候选基因中的互作。总共鉴定到 163 个表观遗传数量性状位点（epiQTLs；LOD≥3.0），解释了 1.7-44.5%的表型变异，这些位点被映射到一个具有 19 个连锁群的高分辨率表观遗传图谱上，该图谱在两个群体中都得到了显著的 MSAP 关联（P<0.001）的支持。有 23 个候选基因参与生长调控和木材形成，它们的标记位于 epiQTLs 中，并与两个群体中的相同性状相关联。进一步的 eQTN 和 eQTM 作图表明，23 个候选基因中的因果遗传和表观遗传变异可能在基因表达和表型中更多地发生在转座子上的互作。本研究为研究树木复杂性状的表观遗传结构和遗传与表观遗传变异之间的相互作用提供了策略。
