Title: Characterization of Chilling Stress Response in Rice Landrace to Identify Variant

Alleles Using Genomics and Epigenomics Approaches

Objectives: To employ a multi-omics approach for generating an in-depth map of the molecular
events that regulate cold tolerance in CB1, at genetic and epigenetic levels.

To identify the altered DNA methylation patterns in cold-tolerant CB1 in the background of
high-yielding variety IR36 which is cold-sensitive

To identify the variant alleles associated with cold tolerance in CB1 using a combination of
genomic and epigenomic approaches

Methodology:

 RNA-seq analysis will be used to identify differentially expressed genes in CB1 and IR36
under cold stress conditions. This will help in identifying the key regulatory genes
involved in cold tolerance.
 DNA methylation analysis using reduced representation bisulfite sequencing (RRBS) will
be carried out to identify the altered methylation patterns in CB1 compared to IR36 under
cold stress conditions.
 Genome-wide association studies (GWAS) will be performed to identify the variant
alleles associated with cold tolerance in CB1, by comparing the genetic variations in CB1
with those in IR36 and other rice landraces.

Expected outcomes:

 Identification of key regulatory genes involved in cold tolerance in CB1.

 Identification of altered methylation patterns associated with cold tolerance in CB1.
 Identification of variant alleles associated with cold tolerance in CB1.
 A comprehensive map of the molecular events that regulate cold tolerance in CB1, at
genetic and epigenetic levels.