DNA methylation is a widespread epigenetic mark that affects gene expression and transposon mobility during plant development and stress responses. However, the role of DNA methylation in regulating the expression of microRNA (miRNA) genes remains largely unexplored. Here, we analyzed DNA methylation changes of miRNA genes using a pair of soybean (Glycine max) near-isogenic lines (NILs) differing in their response to soybean cyst nematode (SCN; Heterodera glycines). Differences in global DNA methylation levels over miRNA genes in response to SCN infection were observed between the isogenic lines. miRNA genes with significant changes in DNA methylation levels in the promoter and primary transcript-coding regions were detected in both lines. In the susceptible isogenic line (NIL-S), 82 differentially methylated miRNAs were identified in response to SCN infection whereas, in the resistant isogenic line (NIL-R), only 16 differentially methylated miRNAs were identified. Interestingly, gma-miR5032, gma-miR5043, gma-miR1520b, and gma-2107-ch16 showed opposite methylation patterns in the isogenic lines. In addition, the miRNA paralogs gma-miR5770a and gma-miR5770b showed hypermethylation and hypomethylation in NIL-S and NIL-R, respectively. Gene expression quantification of gma-miR5032, gma-miR5043, gma-miR1520b, and gma-miR5770a/b and their confirmed targets indicated a role of DNA methylation in regulating miRNA expression and, thus, their targets upon SCN infection. Furthermore, overexpression of these four miRNAs in NIL-S using transgenic hairy root system enhanced plant resistance to SCN to various degrees with a key role observed for miR5032. Together, our results provide new insights into the role of epigenetic mechanisms in controlling miRNA regulatory function during SCN–soybean interactions.

Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

DNA 甲基化是一种广泛存在的表观遗传标记，在植物发育和胁迫反应过程中影响基因表达和转座子流动性。然而，DNA 甲基化在调节 microRNA (miRNA) 基因表达中的作用在很大程度上仍未被探索。在这里，我们使用一对大豆 ( Glycine max ) 近等基因系 (NIL) 分析了 miRNA 基因的 DNA 甲基化变化，这对大豆近等基因系 (NIL) 对大豆胞囊线虫 (SCN；大豆异皮线虫) 的反应不同。在同基因系之间观察到响应 SCN 感染的 miRNA 基因的整体 DNA 甲基化水平的差异。在两个品系中均检测到启动子和初级转录编码区的 DNA 甲基化水平发生显着变化的 miRNA 基因。在易感等基因系（NIL-S）中，识别出响应SCN感染的82个差异甲基化miRNA，而在抗性等基因系（NIL-R）中，仅识别出16个差异甲基化miRNA。有趣的是，gma-miR5032、gma-miR5043、gma-miR1520b 和 gma-2107-ch16 在同基因系中显示出相反的甲基化模式。此外，miRNA旁系同源物gma-miR5770a和gma-miR5770b分别在NIL-S和NIL-R中表现出高甲基化和低甲基化。 gma-miR5032、gma-miR5043、gma-miR1520b 和 gma-miR5770a/b 的基因表达定量及其已确认的靶标表明 DNA 甲基化在调节 miRNA 表达中的作用，因此是它们在 SCN 感染时的靶标。此外，使用转基因毛状根系统在 NIL-S 中过度表达这四种 miRNA 在不同程度上增强了植物对 SCN 的抗性，其中观察到 miR5032 发挥着关键作用。 总之，我们的结果为 SCN-大豆相互作用过程中表观遗传机制在控制 miRNA 调节功能中的作用提供了新的见解。

版权所有 © 2020 作者。这是一篇根据 CC BY-NC-ND 4.0 国际许可证分发的开放获取文章。