# Genotype‐dependent DNA methylation patterns are negatively associated with allelic variation rather than heat‐induced gene expression in two contrasting potato genotypes

## TL;DR

This study shows that DNA methylation in potatoes is more linked to genetic differences than to heat stress effects on gene expression.

## Contribution

The study reveals that DNA methylation in potatoes is associated with allelic variation rather than heat-induced gene expression.

## Key findings

- Most differentially methylated regions were constitutive, not induced by heat stress.
- Hypermethylated regions were linked to lower alternative allele frequencies.
- DNA methylation did not consistently regulate gene expression under heat stress.

## Abstract

Potato (Solanum tuberosum L.) is an important food crop that is sensitive to high temperatures, which cause major changes in the transcriptome and a reduction in yield. In several plant species, DNA methylation has been reported to influence gene expression, particularly under abiotic stress conditions. However, the role of DNA methylation in regulating gene expression in heat‐tolerant and heat‐sensitive potato genotypes is still poorly understood. In this study, we conducted genome‐wide DNA methylome and transcriptome analyses of leaves from two contrasting potato cultivars, Annabelle (moderately heat‐tolerant) and Camel (heat‐sensitive), before and after heat stress (HS). Genome‐wide differential methylation analysis revealed that most identified differentially methylated regions (DMRs) were constitutive, reflecting variation between cultivars rather than being induced by HS. While thousands of heat‐responsive differentially expressed genes (DEGs) were identified, only a small fraction coincided with heat‐induced DMRs. Despite substantial constitutive DNA methylation and transcriptome differences between the cultivars, we found no consistent association between DMRs and DEGs, indicating that DNA methylation does not play a widespread direct regulatory role in gene expression. Surprisingly, hypermethylated genomic regions were associated with lower alternative allele frequencies, whereas hypomethylated regions showed the opposite trend. These findings indicate that the potato DNA methylome is largely stable under HS and that constitutive DNA methylation variation contributes rather to genetic diversity than to the direct regulation of gene expression.

To determine the role of DNA methylation in heat stress (HS) adaptation, two contrasting potato cultivars, Annabelle and Camel, were subjected to severe HS conditions. Surprisingly, we found DNA methylation is relatively unaffected after HS in both cultivars and is associated with allelic variation.