DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea

Mohan Singh Rajkumar,Niraj Kumar Khemka,Khushboo Gupta,Rohini Garg,Mukesh Jain

doi:10.1038/s42003-020-1059-1

Mohan Singh Rajkumar, Niraj Kumar Khemka + Show 3 more

Open Access

https://doi.org/10.1038/s42003-020-1059-1

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Abstract

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.

Highlights

Seed development is orchestrated via complex gene regulatory networks and pathways
To understand the role of DNA methylation in influencing expression of genes involved in seed size/weight determination, we identified differentially methylated region (DMR)-associated differentially expressed genes (DEGs) between the cultivars
Here, we sought to understand the role of DNA methylation during seed development and seed size/weight determination in chickpea via bisulphite sequencing

Summary

Introduction

Seed development is orchestrated via complex gene regulatory networks and pathways. Epigenetic factors may govern seed development and seed size/weight. Frequency of intragenic TEs was higher in CHH context differentially methylated region (DMR) associated differentially expressed genes (DEGs). We identified candidate genes involved in seed size/weight determination exhibiting CG context hypermethylation within the gene body and higher expression in JGK 3. Epigenetic regulation of protein-coding genes and processes involved in seed development and seed size/weight determination is largely unknown. Loss of methylation in CHG and CHH contexts was not found to affect seed development and seed viability in Arabidopsis and no significant role of DNA methylation in regulation of important genes and processes involved in seed development was suggested[26]. Despite no significant correlation between differential methylation and differential gene expression during seed development at global level, a body of evidences have demonstrated regulation of imprinted genes in allele-specific manner especially in endosperm[31,32,33] and determination of seed size/weight in generations via genomic imprinting[32]. The possible role of intragenic TEs in controlling differential methylation and differential expression was revealed

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