Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage
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Date
2021-10
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Abstract
Long intergenic non-coding RNAs (lincRNAs)
belong to the category of long non-coding RNAs
(lncRNAs), originated from intergenic regions, which do
not code for proteins. LincRNAs perform prominent role in
regulation of gene expression during plant development
and stress response by directly interacting with DNA,
RNA, or proteins, or triggering production of small RNA
regulatory molecules. Here, we identified 2973 lincRNAs
and investigated their expression dynamics during pedun
cle elongation in two Indian rice cultivars, Pokkali and
Swarna, at the time of heading. Differential expression
analysis revealed common and cultivar-specific expression
patterns, which we utilized to infer the lincRNA candidates
with potential involvement in peduncle elongation and
panicle exsertion. Their putative targets were identified
using in silico prediction methods followed by pathway
mapping and literature-survey based functional analysis.
Further, to infer the mechanism of action, we identified the
lincRNAs which potentially act as miRNA precursors or
target mimics.