Natural epiallelic variation is associated with quantitative resistance to the pathogen Plasmodiophora brassicae

Clubroot caused by the protist Plasmodiophora brassicae is a major disease affecting cultivated Brassicaceae. Here, we uncover the existence of a natural epigenetic variation that is associated with partial resistance to clubroot in Arabidopsis, by using QTL fine mapping followed by extensive DNA sequence and methylation analyses. We show that at QTL Pb-At5.2, DNA methylation variation is extensive across accessions and strictly correlates with expression variation of the two neighboring genes At5g47260 and At5g47280, which encode NLR-immune receptors. Moreover, these natural variants are stably inherited and are not consistently associated with any nucleotide variation. These findings suggest a direct role for epigenetic variation in quantitative resistance of plants to pathogen attacks.