Differential DNA methylation and gene expression in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.
Differential DNA methylation and gene expression in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.
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番茄和 S. pimpinellifolium 互杂种中的差异 DNA 甲基化和基因表达。
DOI：
10.1093/dnares/dsx028
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发表时间：
2017-12-01
期刊：
影响因子：
--
通讯作者：
Chen L
中科院分区：
文献类型：
--
作者：
Raza MA;Yu N;Wang D;Cao L;Gan S;Chen L
广泛杂交是提高作物产量和质量的常见且有效的育种策略。一个有趣的现象是，互惠杂种通常表现出不同的表型，其潜在机制尚不清楚。在这里，我们报告了通过甲基化 DNA 免疫沉淀测序对番茄、菠菜茄及其相互杂种的 DNA 甲基化模式进行的比较分析。与亲本相比，互杂杂交体的 CpG 岛和 LTR 逆转录元件中的 DNA 甲基化水平较低。重要的是，互补杂交体之间的 DNA 甲基化模式（主要在内含子和 CDS 区域）存在显着差异。这些不同的甲基化区域被映射到 79 个基因，其中 14 个被选择用于基因表达水平分析。虽然启动子区域的DNA甲基化与基因表达之间存在负相关，但基因体区域的关系更为复杂。进一步的关联分析显示，有15个差异甲基化基因与siRNA相关，并且这些基因的甲基化水平与各自的siRNA呈负相关。所有这些数据都提出了一种可能性，即杂交方向诱导了不同的表观基因组，从而导致相互杂交的转录水平发生变化。
Wide hybridization is a common and efficient breeding strategy for enhancing crop yield and quality. An interesting phenomenon is that the reciprocal hybrids usually show different phenotypes, and its underlying mechanism is not well understood. Here, we reported our comparative analysis of the DNA methylation patterns in Solanum lycopersicum, Solanum pimpinellifolium and their reciprocal hybrids by methylated DNA immunoprecipitation sequencing. The reciprocal hybrids had lower levels of DNA methylation in CpG islands and LTR retroelements when compared with those of their parents. Importantly, remarkable differences in DNA methylation patterns, mainly in introns and CDS regions, were revealed between the reciprocal hybrids. These different methylated regions were mapped to 79 genes, 14 of which were selected for analysis of gene expression levels. While there was an inverse correlation between DNA methylation and gene expression in promoter regions, the relationship was complicated in gene body regions. Further association analysis revealed that there were 15 differentially methylated genes associated with siRNAs, and that the methylation levels of these genes were inversely correlated with respective siRNAs. All these data raised the possibility that the direction of hybridization induced the divergent epigenomes leading to changes in the transcription levels of reciprocal hybrids.
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