EPIGENETIC REGULATION UNDER DROUGHT STRESS RESPONSE IN RICE: UNDERSTANDING THE DNA METHYLATION PATTERN
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Date
2020-03-20
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UNIVERSITY OF AGRICULTURAL SCIENCES, GKVK BENGALURU
Abstract
DNA methylation modulates gene expression in plants when exposed to abiotic
stresses. This study aimed to examine the pattern and inheritance of DNA methylation in
rice genotypes under drought. DNA methylation occurring at CpG islands (CGI)
modulates gene expression. The relationship between epigenetic marks (CGI) and gene
expression under drought was analysed using in silico analysis. Promoter regions of
many down-regulated genes showed more than two CGI, and only one CGI in upregulated
genes under stress. To validate this, in vivo expression analysis was performed
using rice genotypes, Apo and IR64 grown under puddled, 100 and 60 percent field
capacity (FC) using genes with (PP2C, PAL, LEA3) or without CGI (HSP70, RH25).
This analysis indicated an association between CGI and gene expression. The importance
of DNA methylation at these sites was studied in rice seedling, Apo, AC39020, BPT5204
and IR64, using 5’-azacytidine (methylation inhibitor) under NaCl and PEG induced
stresses, which revealed that DNA methylation regulates gene expression. To study the
drought effect on DNA methylation, global methylome was performed using MS-RAPD
and whole genome bisulfite sequencing (WGBS). The memory effect was also studied
using the plants retained in the puddled, 100 and 60 percent FC and subjected to different
soil water status in the subsequent generation. MS-RAPD analysis indicated that stress
induced hyper methylation in IR64, and hypo methylation in Apo and the stress memory
was retained in the subsequent generation. WGBS in IR64 indicated differential DNA
methylation in intergenic region followed by promoter region under 100 and 60 per cent
FC. Gene expression analysis using semi-quantitative, real time and nanostring-based
approaches of select genes indicated varied pattern of methylation-associated gene
expression under stress and these patterns were passed to the next generation. The study
highlighted importance of DNA methylation in gene expression under drought and its
inheritance.