Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem

Area of Science:

• Plant genetics and epigenetics
• Molecular plant pathology
• Wheat breeding

Background:

• Wheat leaf rust, caused by Puccinia triticina, poses a significant threat to global wheat production.
• Understanding the genetic and epigenetic mechanisms underlying plant resistance is crucial for developing durable resistance strategies.
• The Lr28 gene confers resistance to wheat leaf rust, but its precise mode of action at the epigenetic level remains largely unexplored.

Purpose of the Study:

• To investigate the role of differential DNA methylation in conferring leaf rust resistance in wheat.
• To compare DNA methylation patterns between a susceptible wheat cultivar and its near-isogenic line carrying the Lr28 resistance gene.
• To elucidate the relationship between DNA methylation, gene expression, and leaf rust resistance.

Main Methods:

• Methylation Sensitive Amplified Polymorphism (MSAP) was employed to assess genome-wide DNA methylation.
• Methylated DNA Immunoprecipitation (MeDIP) was used to enrich for methylated DNA fragments.
• Gene expression analysis was inferred from methylation patterns in gene-associated regions (promoters, exons, introns).

Main Results:

• Both susceptible and resistant lines exhibited increased hypomethylation and decreased hypermethylation over time post-inoculation, suggesting general gene activation.
• The resistant near-isogenic line (NIL) showed significantly more hypermethylated genes and fewer hypomethylated genes compared to the susceptible cultivar, indicating gene silencing in the resistant line.
• DNA methylation levels were highest in intergenic regions, followed by promoters, transcription termination sites, and gene bodies.
• Hypermethylation in promoter and gene body regions did not consistently correlate with gene expression inhibition, suggesting complex regulatory networks.
• MSAP analysis revealed distinct methylation contexts: ^mCG in the susceptible cultivar and ^mCCG in the resistant NIL at 96 hours after inoculation.

Conclusions:

• Differential DNA methylation plays a critical role in Lr28-mediated leaf rust resistance in wheat.
• The Lr28 resistance gene is associated with widespread gene silencing in wheat, contributing to effective defense against leaf rust.
• Epigenetic modifications, beyond simple methylation-expression correlations, are likely involved in the dynamic regulation of wheat defense responses.
• The study provides novel insights into the epigenetic control of plant-pathogen interactions and offers potential targets for breeding disease-resistant wheat varieties.