Seed development is orchestrated via complex gene regulatory networks and pathways. Epigenetic factors may also govern seed development and seed size/weight. Here, we analyzed DNA methylation in a large-seeded chickpea cultivar (JGK 3) during seed development stages. Progressive gain of CHH context DNA methylation in transposable elements (TEs) and higher frequency of small RNAs in hypermethylated TEs during seed development suggested a role of the RNA-dependent DNA methylation pathway. Frequency of intragenic TEs was higher in CHH context differentially methylated region (DMR) associated differentially expressed genes (DEGs). CG context hyper/hypomethylation within the gene body was observed for most of DMR-associated DEGs in JGK 3 as compared to small-seeded chickpea cultivar (Himchana 1). We identified candidate genes involved in seed size/weight determination exhibiting CG context hypermethylation within the gene body and higher expression in JGK 3. This study provides insights into the role of DNA methylation in seed development and seed size/weight determination in chickpea.

种子的发育通过复杂的基因调控网络和途径进行协调。表观遗传因素也可能控制种子的发育和种子的大小/重量。在这里，我们分析了种子发育阶段大种子鹰嘴豆栽培品种（JGK 3）中的DNA甲基化。CHH上下文DNA甲基化在转座元件（TEs）中的逐步增加以及种子形成过程中超甲基化TEs中小RNA的较高频率提示了RNA依赖性DNA甲基化途径的作用。在CHH背景差异甲基化区域（DMR）相关的差异表达基因（DEG）中，基因内TE的频率更高。与小种子鹰嘴豆品种（Himchana 1）相比，JGK 3中大多数与DMR相关的DEG都观察到基因体内的CG上下文过度/低甲基化。