Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice

Area of Science:

• Plant genetics and epigenetics
• Crop improvement and breeding
• Molecular biology of noncoding RNAs

Background:

• Epigenetic variants contribute to phenotypic diversity in eukaryotes.
• Epialleles represent a potential genetic resource for crop breeding, but are underrepresented in rice.
• Identifying novel epialleles is crucial for expanding the genetic toolkit in rice.

Purpose of the Study:

• To identify and characterize novel epialleles in rice related to agronomical traits.
• To investigate the molecular mechanism underlying the observed phenotypic variation.
• To explore the potential of epialleles in rice breeding programs.

Main Methods:

• Identification of a gain-of-function epiallele (Epi-sp) in rice.
• Phenotypic analysis of Epi-sp plants, focusing on panicle architecture.
• Sequence analysis to rule out nucleotide variations in the ESP gene.
• Bisulfite sequencing to assess DNA methylation status in the ESP gene's transcriptional termination region (TTR).
• Analysis of ESP gene expression in Epi-sp and wild-type plants.

Main Results:

• A novel epiallele, Epi-sp, of the rice ESP gene was identified, leading to a dense and short panicle phenotype.
• No nucleotide sequence variations were found in the ESP gene of Epi-sp plants.
• Hypomethylation in the TTR of the ESP gene was observed in Epi-sp plants, causing ectopic gene expression.
• Specific methylation patterns of 26 CGs and 13 CHGs within a 313-bp region were found to be critical for ESP expression regulation.

Conclusions:

• Epi-sp represents a unique rice epiallele with significant implications for panicle architecture.
• Epigenetic modification, specifically hypomethylation, of the ESP gene regulates panicle development in rice.
• This study highlights the potential of exploiting epialleles for crop improvement and breeding in rice.