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.

Rajkumar et al. report progressive gain of CHH context DNA methylation in transposable elements during seed development in chickpea, of which hypermethylation is associated with small RNAs. The candidate genes that determine seed size/weight in chickpea show CG context hypermethylation in the gene body and higher expression in large-seeded cultivar.

Details

Title
DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea
Author
Singh, Rajkumar Mohan 1 ; Gupta Khushboo 2 ; Khemka, Niraj Kumar 1 ; Garg Rohini 2   VIAFID ORCID Logo  ; Jain Mukesh 3   VIAFID ORCID Logo 

1  Jawaharlal Nehru University, School of Computational and Integrative Sciences, New Delhi, India (GRID:grid.10706.30) (ISNI:0000 0004 0498 924X) 
2  Shiv Nadar University, Department of Life Sciences, School of Natural Sciences, Gautam Buddha Nagar, India (GRID:grid.410868.3) (ISNI:0000 0004 1781 342X) 
3  Jawaharlal Nehru University, School of Computational and Integrative Sciences, New Delhi, India (GRID:grid.10706.30) (ISNI:0000 0004 0498 924X); National Institute of Plant Genome Research (NIPGR), New Delhi, India (GRID:grid.419632.b) (ISNI:0000 0001 2217 5846) 
Publication year
2020
Publication date
2020
Publisher
Nature Publishing Group
e-ISSN
23993642
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s42003-020-1059-1
ProQuest document ID
2419779831
Copyright
© The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.