Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis

Abstract

Variation in DNA methylation enables plants to inherit traits independently of changes to DNA sequence. Here, we have screened an Arabidopsis population of epigenetic recombinant inbred lines (epiRILs) for resistance against Hyaloperonospora arabidopsidis (Hpa). These lines share the same genetic background, but show variation in heritable patterns of DNA methylation. We identified four epigenetic quantitative trait loci (epiQTLs) that provide quantitative resistance without reducing plant growth or resistance to other (a)biotic stresses. Phenotypic characterisation and RNA-sequencing analysis revealed that Hpa-resistant epiRILs are primed to activate defence responses at the relatively early stages of infection. Collectively, our results show that hypomethylation at selected pericentromeric regions is sufficient to provide quantitative disease resistance, which is associated with genome-wide priming of defence-related genes. Based on comparisons of global gene expression and DNA methylation between the wild-type and resistant epiRILs, we discuss mechanisms by which the pericentromeric epiQTLs could regulate the defence-related transcriptome.

Surviving in a Hostile World: Plant Strategies to Resist Pests and Diseases

“…by which disease-induced DNA hypomethylation is transmitted to following generations to control TAR. This hypothesis is supported by Furci et al (49), who identified hypomethylated DNA regions that control quantitative disease resistance and that are stable over multiple generations. Furthermore, mutation of the DNA demethylase gene ROS1 not only affects basal resistance to biotrophic pathogens (155) but also prevents TAR in progeny from diseased plants (81).…”

“…Recent evidence has shown that sRNAs can trans-activate defense-related genes through interaction with ARGONAUTE 1 (AGO1) and the SWI/SNF chromatin remodeling complex (79). Further support for trans-regulation of defense gene priming came from a recent study of Arabidopsis epigenetic recombinant inbred lines (epiRILs), which identified four hypomethylated epigenetic quantitative trait loci (epiQTLs) that control quantitative resistance against downy mildew (49). Transcriptome analysis revealed that the most resistant epiRILs were constitutively primed to activate defense-related genes.…”

“…For instance, a better understanding of the epigenetic underpinnings of TAR can aid the generation and selection of epiRILs that are constitutively primed for defense. In Arabidopsis, this approach allows the selection of lines that express quantitative disease resistance without affecting plant growth (49). Whether this approach is suitable for crops depends on a variety of factors, including the stability of the resistance and potential nontarget effects.…”

Whole-Genome Methylation Analysis Reveals Epigenetic Variation in Cloned and Donor Pigs

“…A binomial distribution test was performed to identify 5mC for each C site, and then the P value of binomial distribution test was subjected to false discovery rate (FDR) correction using the Benjamini & Hochberg method in the p.adjust package of the R software. The C site with coverage > 4X and an FDR < 0.05 was considered to be a true methylation site (Zhang et al, 2017b;Furci et al, 2019).…”

Position-dependent effects of cytosine methylation onFWAexpression inArabidopsis thaliana

“…Genomes of met1 mutants are largely hypomethylated at CG dinucleotides that usually inherit cytosine methylation faithfully during DNA replication through MET1 activity (5) . Phenotypic abnormalities do, however, not require whole-genome changes in cytosine methylation, as a recent study describes how hypomethylation at a few select loci is sufficient to establish quantitative resistance to a pathogenic oomycete, Hyaloperonospora arabidopsidis (Hpa) (6) .…”